Right now there is only one field pointing PCGen where to find output sheets.
My suggestion is to have two, just like for data directories: "PCGen Data Directory" and "PCGen Custom Data Directory". When I choose which data sources to load PCGen displays all the options in both locations. This allows me to store my custom data in a location separate from PCGen. And then each time I install an updated version of PCGen I do NOT have to copy my custom data into PCGen's folder structure.
I'd like the same behavior for output sheets.
I'm about to create a custom output sheet (one that does a stat block showing the cost of each possession--very helpful for my campaign). However, because there is just one location pointer field I will have copy my custom sheet to the appropriate folder deep within PCGen each time an update comes out.