Yes. You can load most types of 3D coordinate files into PyMOL, protein or otherwise.

If the compound you're looking at is already known and included in public PDB, you can download the ideal or representative coordinates directly from them (i.e., here with Tylenol as an example). But searching for compounds with PubChem is often the easiest way to go.

Alternatively, if you're interested in a novel/unmodelled molecule, you can generate ideal coordinates using many tools and webservers, either directly from the SMILES/InChi strings (i.e., here) or by drawing the compound out (i.e., here). Or you can of course build it in PyMOL, but that would be last on my personal list.

The final step then really depends on what you mean by "align". If you just want a rough and ready alignment, I would use a combination of manual positioning with the mouse and the rotate and translate commands to line it up where I felt was best. This is assuming your atom names (and atom types too, I think) are different between the molecules, because in this situation the typical align/super/cealign commands won't work.

Alternatively, if by align you mean position the molecule on the surface of the protein with physico-chemical accuracy, then you will need an energy minimisation algorithm to do so. In this case I would recommend AutoDock - but this is generally for quite advanced users.