Wich battery configuration I should use to supply raspberry, arduino and stepper motors
We did something similar back in college for the IEEE micro-mouse competition.
Chris Stratton is correct in that I wouldn't mess with Lithium batteries just yet.  Use a bunch of NiMH batteries, as they are robust against shorting (though the wires may not be!) and easy to charge.

I think for my project I used about 8 AA batteries in series with a buck regulator to step it down for the CPU. We used a micro-controller to drive stepper motors drivers which drove the steppers directly from the battery.  We would get about 30 minutes of dev time per charge with this configuration.

Now in your case you have some power hungry computing specified, so you may need to do a little math:
Estimate your instantaneous power draw. \$5v*2A + 3.3V*0.1A + etc... = ?W\$.

Most NiMH are around 2000mAh. So 8 in series gives you \$1.2V*8*2Ah=19.2Wh\$

Finally divide your estimate by your battery pack to get a time estimate:
\$\frac{?W}{19.2Wh}=?h\$