Lots of home mechanics on these forums work on Di2 shifting systems.
If you don't feel confident then bring it to the shop. Having said that, it isn't very difficult if the directions are followed and the mechanic's warning not to mess around with it should be taken with a grain of salt. It can be messed up but it won't break and can easily be reset to factory default so that you can start again.
The first place to start with anything Shimano is the Manuals & Technical Documents website.
Manuals & Technical Documents
The second resource needed is the E-Tube Project website which is specific to Di2.
http://e-tubeproject.shimano.com/
Look up your system at the Tech Docs website. The Dealer Manuals will give complete setup and maintenance procedures and these will give you a better idea if it is something you want to tackle or not.
Adjusting limts and index on a Di2 system isn't rocket science or black magic. It is basic maintenance and I would encourage you. Look at the dealer manuals and let us know if we can help.
My own personal opinion is that for most people with basic mechanical aptitude, lack of a proper bike repair stand is a more important factor then is the prospect of messing something up when deciding whether a bike should be brought to a shop. It is an order of magnitude more difficult to work on shifting systems without a repair stand. There are many on craigslist.
-Tim-