So I was thinking, would it be better to flip the growing terminal upwards later on, or turn it into a branch and grow an apex from what is currently the top of the tree?
I think your tree is far too young to be making such decisions. Pruning is a big part of developing bonsai and I'm pretty sure you will cut off a whole lot of what is there now as this tree develops.
One problem with leaving a large, strong section like the current leader as a branch is that it will grow much faster than any apex so you'll end up with a small top and a big branch which does not look so good.
This appears to be J. procumbens which normally grows horizontally as ground cover so that terminal will grow faster than most other parts and will grow out and downwards unless you stop it by pruning.
The little branches are way too thin and delicate for learning to wire. Most are likely to break off if you try so best to let them all grow for a year or 2 before thinking about any branch placement or shaping.
Do you have any idea how big you want this bonsai?
Trees can just be allowed to grow and develop haphazardly but I find it helps to have some sort of vague idea of what you are trying to achieve. Knowing what you want to achieve helps direct the techniques and processes you use while developing the bonsai.
Based on this little juniper I'm guessing you are quite new to bonsai so may not understand some key concepts yet.
Little trees in little pots tend to grow really slow so it takes many years to grow a really good looking bonsai.
Trees in larger pots grow bigger quicker. We can then cut off excess and downsize the results to a bonsai. This requires letting most parts grow long so the tree won't look 'bonsai for a few years. Not much point worrying about pruning some parts during this phase of development.
Starting with little trees or seed can be cheaper and fun but it is usually the slowest way to achieve a good bonsai.