Applying an armature modifier and making vertex groups work?

So I added an armature modifier and selected the armature to deform like usual.
The vertex groups and everything else were working fine.

After I applied the modifier, every vertex group and bone stopped working/moving when I tried to test moving the bones in pose mode.

Help?

I’m trying to get rid of the modifier as well as making the vertex groups work at the same time because I’m trying to export the model to SMD using SMD tools but the SMD exporter gave me a warning.
It said that it ignores the armature modifier because my model already has an envelope.

So I’m trying to find a way to fix this problem.