Tom you can have different folders for your symbols and padstacks but you would have to edit the PSMPATH & PADPATH to tell the system where to look. In Allegro go to Setup User Preferences then go to Paths, Libary.
When you create a package symbol for a footprint there will be 3 files created. .DRA, .PSM, .TXT. You will also have the padstacks used for that particular symbol. What I do is keep the pads,dra,psm, .txt files for each symbol in the same folder. This has helped me cut down on packaging problems when creating a board from the schematic.
By way of an example here is directory structure.
PSMPATH is configured to point to the following "Click expand in that dialog box first" and remove any paths you do not need before making your edits.
PADPATH is configured the same but I also include a folder for vias, again "Click expand in that dialog box first" and remove any paths you do not need before making your edits.
When you create your symbols dont use spaces in the name as it will lead to packaging problems. For example SOT_23.dra,SOT23.dra are all ok to use.
Be aware also that it is possible for Allegro 16.5 to blow away your custom PSMPATH and custom PADPATH and replace them with system defaults. I kid you not. This one seems to be a bug. My work-around for this is to make the env file read-only after all edits have been made. Depending on your setup you may or may not come across this hidden treasure, hope you dont : )