Welcome to the site. Starting bonsai from seed is very long process that has the potential to fail in so many ways that I don't really suggest that new growers take that approach.
When I start seeds I always start as many as I can get my hands on. This is because the process of taking any one seedling all the way from germination through to anything that resembles an actual bonsai will take a decade or so. Depending upon species and the desired outcome it could even take much longer. During this time many will fail for many reasons.
Many seeds don't germinate, those that do need to be transplanted and root-pruned presenting the opportunity for more losses. Then there are pests to contend with, insects, herbivores, and disease. After all that not every plant seems to 'have what it takes' to be a good bonsai. Some just want to cooperate. Each year expect to lose a few for any of the reasons listed above or numerous other problems that can plague trees. Every year you need to pot them up, increasing the space required to keep the larger pots in. This means more soil, more fertilize, more watering and overall, more work.
In short I would say start with many and in ten years you might have a few decent specimens. Still sound appealing? Bonsai kits make this sound easy, it's not. Of course many growers, myself included, do start seeds but it is not quick or easy to get from a seedling to a bonsai.
A better approach would be to spend a little money on an established plant. Even if it is a low end piece of material, that will allow you to get a better idea of what bonsai is all about. There is the daily care involved such as placement and watering. There is re-potting and fertilizing to learn about as well as what constitutes a decent, free draining, bonsai mix. You can still keep your seedlings, they will be a great learning experience.
WRT your situation, many trees don't do well inside without knowing what your seedlings are you are at an immediate disadvantage. Can you post pictures? This would help us to help you.
Yes, they will need separated, I just did this with a flat of Quince and got enough to fill a 32 cell nursery flat with a few to spare. I trimmed the tap root from each one to encourage lateral roots and potted in a gritty mix. I did not lose one, yet. Don't over-pot them greatly, choose an appropriately sized container, probably around two inches. I would not trim the roots on yours unless they are too deep for the chosen pot. If they are too long you can go ahead and trim them to allow them to fit. Without knowing the species this can be risky but this goes hand in hand with what I was saying above, expect some losses.
Since you posted this is the indoor section I wonder if you are intending to grow bonsai as an indoor venture? As I mentioned above not all species are suitable for indoor growing. Some will do fine, with proper care, and some will almost surely die.
I don't want to discourage you and we will do what we can to help but it is always best to know what to expect realistically.