I am trying to find a used motor for my 95 civic. I had some questions about what type of motor I can use. Does it have to be the same stock motor in order to line up with the transmission? Or could I put in a 1.6 vtec or a B16 or B18 motor? Will these motors line up with my stock transmission?

Same year and model would be easier.
If you Find Nice Motor that fits, Make sure you get associated electronic system parts.
If you don't get them then, you will probably have to get later.
I would get manual for your own car and look at prospective Engine Manual and compare
Talk to a couple of Honda Mechanics. If getting cars side by side for comparison not possible. Take pictures of your Engine and parts layout, compare.