Well I always just compile manually, but perhaps you could do it using the import tool. You'll need to get the name of the mdl file you want to replace. Let's say it's the bloke's bucket hat. When you compile your model, you'll want to rename your .mdl and associated files (.dx80, vtx, etc.) into exactly what the bucket hat's name is (which should be sniper_fishinghat.mdl). Put these files into a folder structure that mimics the VPK files (models/player/items/sniper). Do the same for the materials.

Then you'll want to turn your materials and models folders into one VPK file which you can put into your custom folder. Create a folder that you want your mod to be named (example: Bubbles). Put your materials and models folder inside this folder, and then drag the Bubbles folder into the C:\Program Files (x86)\Steam\SteamApps\common\Team Fortress 2\bin\vpk.exe application. This will automatically make a VPK of the folder Bubbles. To install the mod, all you need to do is drag Bubbles.vpk into your C:\Program Files (x86)\Steam\SteamApps\common\Team Fortress 2\tf\custom folder.

The only issue is that the in-game compiler not allow for this to work because the material path might be messed up if you try to change the folder locations. I'm fairly certain the compiler compiles both a workshop folder mdl and a regularly located mdl. Check to see if you can use the regular file location mdl.

Thank you for the helpful information. Just one more question. This is probably an stupid question but where can you find the mdl files of the in game hats?

I've made a hat using the old process without the import tool before, but that was a while back. I think I still have the essential programs to compile it that way.

The in-game hat models are located in the tf2_misc_dir.vpk file in the C:\Program Files (x86)\Steam\SteamApps\common\Team Fortress 2\tf folder. You'll need GCFscape to open the vpk, and when you do, navigate to the models/player/items/classname/ folder for mdls.

Thank you very much Helljumper. I've got to say that you've been very helpful for not just me but for everyone who wanted to make hats but couldn't find out how. I can't express how grateful us modelling novices are to your services