This question boils down to: How do I stay in power? Well, if there is a surefire answer, revolutions would never have existed in history.
Nonetheless, I'll offer the best answer I can. First up, some basic principles.
To stay in power, you must not lose it. Considering that you do not intend to abdicate, the only way that will happen is if it's taken from you against your will. This threat can come from three sources: The masses, the nobility, and foreign powers.
First of all, the people is the lifeblood of every nation. There are two influences to public order. The carrot is how well the people are treated, and the stick is how effectively unrest is suppressed. If all else fails and disorder breaks out, then care must be taken to prevent unrest from turning into riots, riots from turning into revolts, revolts from turning into rebellions, and rebellions from turning into revolution. Dissent is the rake that sows the seeds of rebellion.
Second are the nobility and the dirty game of politics. Unless you are self-replicating and of a single mind, or mentally omnipresent, you'll need to delegate responsibilities to govern effectively. That's what bosses and politicians do. Those responsibilities translate into power, authority and influence. Choosing the right people for the job is important, as is guarding against those who pose a genuine threat. Politics is complex, so I won't go into it.
Finally, foreign powers. This is a matter of warfare, so it's fairly straightforward what you need to do, although the art of war is one of the oldest and most complex disciplines on record.
In conventional civilisations, the key to staying in power tends to be military might. Revolutions are usually won when the military joins the rebels. Coups are dependent on military backing to succeed. Foreign invasions generally come down to a duel between numbers, training, equipment and experience (it is the rare general that wins entire wars with tactics and strategy alone while constantly at a material disadvantage). A good military - and keeping them on your side - depends on mainly money but also political charm.
With those principles in mind, here's a few considerations about your particular situation that I would point out:
- Can non-magical folk develop technological means to match magical folk in what they can do, especially in combat?
- Most of your society is made up of magical folk. If they are anything like human nature, the non-magical folk will suffer severe oppression and discrimination as the inferior race. How will you survive their perpetual anger at their own fates?
- Can magical folk be born from non-magical folk? Such "Mudbloods" can grow up with different mindsets from other magic folk. Some may potentially blame you for their parents' suffering and seek to settle scores somehow.
- Do you possess magical powers too? How can you resist unrest from magical folk?
- Over time, how will your civilisation advance? In the real world, the introduction of gunpowder to Europe helps centralise power in the monarch as he becomes militarily superior to and independent of medieval lords and knights (only the national budget can afford an army's worth of cannons to bulldoze castles with). Does this happen in your world? How does it compare against magic? How will this change dynamics with non-magical folk, and the balance of power with the nobility?
- In other words, how will you keep up with the times?
- Are other worlds capable of invading at all? What do they possess compared to you? Is magic unique to your nation?
- How effective is your national infrastructure? Rapid communications and troop movements can matter a lot. Are you a coastal nation? How deep inland do you go? How fast does news travel, and how rapid can your armies respond to threats?
There's a lot more to consider. A lot can happen in a thousand years. It all comes down to who holds the most power and possess the key to sustaining it.