"On the other hand, I think synaptic (via apt) does install rpms, so does that mean that the rpm dependancy database will be OK?"
Yes. Synaptic uses the rpm command as a service routine.
"On top of this, what happens if I install something (like fluxbox) via a compile? Does that mean it never appears in the rpm database?"
Yes. I solve this problem by using checkinstall to convert tarballs to rpms and then install the rpms. The procedure is similar to the usual compile procedure:
Then install the rpm.
Be prepared. Create a LifeBoat CD.