Actually, eyes are not directly part of the .smd/.dmx mesh (as far as I know), due to the shader (for the material, after compiling) overwriting the UV coordinates. One just has to include a unique material for each eye, and define them in the .qc, and then the rest will be handled by the Source Engine.
Though, exactly what is your problem?

Are you using qc_eyes.exe? It should be in your engine folder.

Okay, so the eyes work in HLMV. But they get distorted in garry's mod when the model is used as a player model as well as sometimes when the eye poser is used on the ragdoll. I'm also having problems with a mesh deformation around the pelvis, as some verts just stop being bound to any part of it. The especially strange part is that the strange deformation stops when I use the model as a player model. I request that anyone wishing to help would message me instead of replying to this thread, then once it's finished we can post the solution for other people so the thread doesn't get messy.