Is there a recommended website or software used to combine photos into a "virtual tray"? Or do folks just do it manually?
I do it manually in Photoshop. Time consuming depending on the coins being added but I don't do it often. Google Gimp, free photoshop like program and just google how to combine images with gimp.
If you want to do a tray, start with a very important decision. Will you want to show coins in proper relative size to each other or are you OK with obols being the same diameter as dekadrachms? If you want proportional sizes, it is a lot easier to shoot all the coins at the same time than to try to adjust them later. I use Photoshop Elements (full Photoshop is overkill for what I do with software). Proportional: Forced to same size: