is it possible to change where a train stops in a station (end or middle) in the config file? if so what am i looking for or does it depend on the particular station?
It's station dependent. The only ones I know that can do this are the Station Platforms series by Bloodnok (James Moody) or the AJS Invisible Station series by andi06.
Or you can use trackmarks and door control commands. That's the way I do it. It takes a bit longer to get it to look decent but once it's set-up it looks good