For me I found "Auto" to give some surprising and unpleasant results - often "Auto" was fine - sometimes great. The D3100 has great dynamic range and thats where I think "Auto" worked best - but use your focus points well and experiment, practice so you know what to expect from your shooting.
I strongly suggest reading as much as you can about the camera and shooting the heck out of it to get used to how it works and learn what works for you. Back in the days of film I always shot manual. However, the D3100 only has one command wheel so changing aperture requires some dexterity.
The "kit" lens that comes with the D3100 has excellent optics - and focuses very close.
I hope this helps. Its been over a year since I shot with the D3100. I found it to be a very great camera for the money.