The process is exactly the same as any custom content for the mod: Place the custom assets in the corresponding folder in your mod's folder.
If you've already started working on your mod, you should have a folder at
.../Steam/steamapps/common/Half-Life/<your_mod>
.
Any custom models should then be placed in
.../Steam/steamapps/common/Half-Life/<your_mod>/models
.
This way when you launch the mod, it'll use the custom models instead of the vanilla models.
You can check out
Tutorial: Setting up a Mod: Part 1 - Mod directory and liblist.gam (Steam) for more information about setting up a mod.