It doesnt matter where the .mdl file goes! You have to browse for it anyways when you use Object Manager. You import models (blp and mdls) into the game. Then you just simply select Custom, and place a unit onto the field. Test the game, move him around, attack a unit. This will make sure that the model file does everything it is supposed to do (PROPERLY!
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Btw, If you had any map related questions, this thread should be moved to the Map Development section (if any1 reads this, do it plz ^_^)!