(Sorry if my english gets wrong sometimes, i'm not a native english speaker.)
Medieval tactics on the battlefield, consists on concentrated regiments with armed soldiers with specific traits, weapons and tasks. REMEMBER THAT Medieval warfare is very different from the modern warfare introduced by Napoleon.
And so you want combine some kind of guerrila warfare into medieval wars? That is possible. Lets start from the very begining...
1 - How to build a rebel army
Who will sponsor this army? The dissatisfied nobility; the own people helping by sharing the crops and money; a foreign country enemy to the current governement. An army needs food, money and equipment to survive. You can decide who will sponsor the army.
How to recruit? A rebelion uses differents methods of recruinting depending on how the war is going. They can recruit people in the largest cities in hideouts; they can recruit at the farms; they can recruit people on the road; they can do it in the conquered land (If the rebelion has managed to get some)
Where they will sleep? HQs and army encampaments has to be somewhere. Where else would it be if not on the remote places? Caves, mountains and swamps are good places. Guerrila armies are easy to pass through these places (but they are not imune to attrition.)
How to feed the army/give the equpment/payment? Clandestinity and piracy are the key-words here. There can be assaults on caravans and shipments. The people responsible to sponsor the army will provide the
The ideology. I think this is the most important you should be asking. Try to imagine what the recruiters will say to inspire the villagers and citzens to the cause, thats their ideology. The vietnans used the rethoric of "freeing Vietnam from capitalism." But this is medieval times, isnt it? The ideology here is more attached to tradition and/or religon. Maybe you could relate to the old times or maybe you could create some legendary hero that is inside the rebelion. "I've joined the rebelion because of Kelsier, he survived the tirany of the king with this incredible powers! He is the only one who can defeat him!"
2 - How to fight this war using guerrila
The strategy. The main aspect of a guerrila is the occultation of the army and its movements. Propaganda were also played an important part on this kind of warfare, because the rebel soldiers are basically villagers, and the people need to feel anger and courage to fight aganist the system. You can get inspiration from the American Revolution, where they've used small attacks to damange the british army. The americans lost the larger battles, but with night attacks on small convoys and important shipment and caravans, they've managed to win the war.
Fighting the own country. Different from the american revolution, the enemy isnt an empire with its capital far from your land, isnt it? The conflict could happen through many, MANY years or just some if a treaty is signed. So, what is the goal of the rebellion? Is it to free a part of the land? To take control of the country? The goal will affect on how the rebelion and the kingdom see the war. The main weapon of the rebelion will be its legitimacy and the ideology on it. If the rebelion loses the people, he loses the war. If the people still belive on the rebelion, the war can continue forever.
Small battles. They will be the key for the success of the rebelion. The goal is not to attack directly the kingdom and destroy it with a single blow, but with bleeding. Make the country bleed. Attack caravans and shipment, destroy their farms and kill their commanders.
Large Battles. The guerrila wants to avoid this. They know they cant fight with an army.
Besieging a city. This can be easily arranged with engineering, may it be with basic rams and ladders or catapults and trebuchets. But I suppose that the wizzards in your world are scholars, they could be the siege engineers and the magical engineers. Maybe they could do something cool with a system of runes into a battering ram, a catapult. And with the rule number 5, you gave on the post, anyone can operate the machine. Remember that a siege can last months, even years, so logistics are important here.
3 - How would medieval tactics have changed if guerrilla warfare had become common?
The main question is: how should we preserve the spirit of a guerrila warfare? That is: the occultation of an army and its movement? How to split the army wihout losing it? How to inspire the people to fight through propaganda? And the most important, how to defeat the enemy? All this, under the conditions of your world (And you world will play an important part for a possible "medieval guerrila.")
The enemy. It would be useless to discuss the guerrila wihout considering of how the enemy is. His empire is vast but his governement is centralized? Why is that? The capital is the only place on the empire with higher culture and resources? Why the other cities dont have similar importance? Geographical limitations could be a good solution for this (or just something else.) Remember that the advantages the guerrila uses, the kingdom could use too. Technology and magic could be used to solve the limitations that medieval era imposed.
Hiding the rebel army and organizing it. Hiding is not the problem, the problem is comunication and logistics in general. Technology and/or magic could solve this. Maybe the wizzards can make contact through telephaty or magic globes. Maybe the supplies could be arranged with magical creatures that manage to drop the supplies by land, sea or air.
Inspiring. Stories are important, in medieval times, your hero(s) would probably be considered as demigods. Religions and beliefs were build by oral traditions, stories that the elders and travellers say about the mysterious events, persons and creatures of the world. There must also be a reason of why the villagers will abandon their hoes and pick up swords to fight aganist their lord and king. Maybe the people are not servants, but slaves, maybe you the kingdom make the people pay high taxes.
Bleed the enemy. Maybe this society is more advanced and the governement is more centralized. The kingdom depends on foreign trade and agriculture is not very dependable on people, which allows more migration into the cities.
Medieval warfare. The runes and mages could play an important role on leading the groups and armies. Attacks on cities would be more common and nobles and lords would start to pay their alligeance to a new leader that wants to take the throne.(The guerrila kind of warfare would still be a problem depending on the economy, because the rebelion shouldt be able to bleed the country if the economy is mostly driven by agricultre.)
How to destroy the enemy? Conquer his land and capital, and you will achieve victory in defeating him. This can only be achieved when the king is weak. (But if during the war, a powerful lord manage to take the throne?)The problems could emerge later with possible lords and nobles that didnt allied to the rebelion that declare themselves kings or pay their alligeance to other king.
But anyway, what would change? That depends directly on how your world will be. My answers will help you to avaliate these simple questions like... how is the king? How its kingdom? How the people live? What they belive in? etc...
You should be worried on how to preserve the medieval identity and the guerrila warfare identity. (But this would be another topic isnt it? :v)
For your inspiration: Brandon Sanderson uses a perfect example of how to build a rebel army in his book series, Mistborn. The Elder Scrolls V Skyrim can also provide you with some inspiration with the stormcloaks.
There is also this video of how the roman army is organized.