Final steps in device manufacturing - AVR programming and board assembly
Most PCB assembly houses (for large volumes) can program microcontrollers before shipping, but you may need to provide the programmer. They can take your files (BOM, gerber etc.) and produce everything for you.

Since you are a self-claimed novice, I recommend listen to How to Bring Your Project from Idea to Reality: Make a Living Doing What You Love from Mitch Altman. It is a ca. 1 hour talk, which covers a lot of things.