in detail, what I assume you call the latest 1.13 version from 2014 is probably 7609 and pretty outdated,
i.e. tons of features missing compared to current version, find a dld link and info here: http://thepit.ja-galaxy-forum.com/index.php?t=msg&th=20380&start=0
Note the creation of "official" respectively "stable" versions were abandoned,
and despite the exaggerated warnings in 1st message by author depressives brot,
these are the new stable versions.
Note also that some features are quite ... well, dangerous,
so you may want to check the thread "flugentes magika workshop" on same forum for some info on these.
last not least, make sure to apply the patch(es) you find in the \docs folder of the extracted archive,
at least if you run the game under a buggy OS, aka win 7, 8 or 10.
What does that mean about "Don't install in program files?" Will it basically overwrite anything in the direct folder it's in? I have I think my gog folder in my data drive(not boot drive) and I just put things as program files for my E drive so I just had to change one letter to easily install things. So would it hurt if I installed it in my gog(galaxy I think) file folder for jagged alliance?