Uh, I dunno where to start. So I'll start with this:

I made a custom model for an scp and it appears too big.

So you might say "Scale it down" or something like that, but here is where the problem comes in.

I scale it smaller in FragMotion and guess what. made no difference ingame whatsoever. it just appears as though i didn't touch it.

Any help would be much appreciated.

Tried scaling it through the game? If this model is for an npc, you can change the scale of the model in the NPCs.ini file in the Data folder. If it's an item you need to change the scale of the model in the source code.