Just bought the Sony NEX-6

IMO, keep it simple to begin with but flexible. Even if you don’t care for RAW files right now, I would advise to use RAW+JPEG mode. Back up RAW for a later date you might want to re-visit and develop the images better than your camera’s JPEG engine can.

Among other major settings, I prefer:

-Set high ISO NR to weak or off (whichever is available)

-Long Exposure NR to off

-Turn “smile/face detection” off unless you feel a need for it

I also, mostly, shoot with local or spot focusing (as opposed to wide), generally keeping it in AF-S mode. I use AF-C only when shooting action, to track.

As far as additional lenses/accessories go, what is your budget? Do you want to enjoy the pleasures of manual focusing? If you want to get into macro, getting Sony LA-EA1 adapter will be a great idea. It will pay for itself (as would LA-EA2 as well but preferable if you want to spend more initially and want DSLR-like auto-focusing). Although, for macro, you have plenty of inexpensive options from just about any mount. And of course, MF is very inviting with your camera featuring Focus Peaking.

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Sony A55, Sony NEX-3, Sony F828