I'd say an FTL capable civilization would progress militarily in a manor close to us.
I mean sure we can argue but I don't think any human can truly write an alien, like 100% alien, culture so we will just advance what I think we would do if we got almost unlimited tech.
Intelligent life is all about surpassing manual labor. And so is warfare.
So their size matters little.
And you have to understand that limitations on our own mechanical contraptions is imposed because either we don't have the tech or we have to put humans in their.
I mean we have stuff like Battleship cannons who are very powerful but have to be mounted to a battleship. But imagine if we can scale down the size, and all other negative stuff, but retain the exact firepower. Would we have soldiers running around with hand held weapons that can destroy a block at 20 kilos?
Only if the military can afford it.
So another limitation. The dreaded budget. Here I highly recommend terrible writing advice.
For example the perfect tanks?
A hoovering monstrosity the size of a building, why not a 100 meters, with plasma, or better, cannons and sophisticated AI, or something similar, that is also equipped with void shields and a meter thick armor.
Add a lot of anti air guns. A bunch of super advanced drones for reconnaissance and urban combat. Then connect units of 3, or more whatever, of them into a network to control the local battlefield.
Lastly add teleportation technology so you can simply use your teleportation network to achieve firepower superiority whenever is needed.
But it's too big, it's too expensive, it's too overkill.
Nah. We have the resources of the known universe, nothing is too big and there is no kill like overkill.
This type of warfare is starting to sound futuristic. Not humans with laser guns or whatever.
In fact the removal of the human, or alien, element is the ultimate goal here.
So if your aliens posse such technology the entire fleet can be commanded from a single ship with the AI, on whatever level, controls thousand of such terrifying machines.
In fact introduce titan like, titans from Warhammer 40K for extra cheese, command units which is basically a super advanced AI with the entire military history and theory of the entire aliens race in their memory.
It also functions as a mobile fortress of absolute insane power.
Seriously read the wiki.
Anyway this is beginning to touch on ground warfare.
But you might ask. Wait a minute. Why would the do that to begin with?
Well because they have a comparable history and since we established FTL travel then, I'm guessing since your world might only include 2 intelligent races, it stand to reason that there are other races and many many planets with even races that are giants.
So with that in mind, again comparable history and other races, it only makes sense for them to make their military in such a manner where either the size is small but a 2 meter tanks can destroy a whole country, or they push their sizes and their tanks are a 1000 meter tanks that also can destroy a country.
Point is go small or go big. Firepower is present in dangerous amounts.
But if you have FTL travel unlocked can't you accelerate a bunch of metal shards to something like I don't know 80000 the speed of light and throw that at a planet?
Huge plasma cannons. Asteroids.
Honestly the book of crazy science fiction, or fantasy, weapon can include insane stuff.
Black hole making ships. Super heating or super cooling the entire planet.
Heck. Our own little race posses enough nuclear bombs to destroy us.
And all that without getting into stuff like chemical or biological weapons. Nor are we talking about super viruses for the lulz.
Honestly if we let our imagination run wild we can destroy the universe faster than you can say what.
So my answer is that they can win.
Of course they can lose.
Imagine stargate like technology but on a larger scale. That race found a floating stargate on their moon on in their orbit. They constructed something similar to our current spaceships and upon entering they are simply teleported into another location. Whatever that tech is. Like is it a network you can navigate or a fixed type traveling.
Anyway once they arrive they are no better equipped than our current spaceships.
Obviously you can move up and down that scale. From can split the planet in half or have to relay on windows vista for FTL travel.
So honestly think what you want to do with the story and work from there.
And more context on the aliens is also welcome.