I think the advice is to offer the second side once your DS has come off the first side by himself and "finished" it (ie has let go of the boob himself rather than just slipping off, coming off because he needs a burp etc), and it's up to him whether he takes a second boob or not. This is what I've done with my DS and it's worked for us. Having said that, if your DS does seem satisfied after one, is starting to gain weight nicely (normal for babies to dip up to 10% of birth weight in the 10-14 days after birth as long as they then start gaining again), is having plenty of wet and dirty nappies and is bright and alert when awake (which will probably only be for quite short period at 2 weeks old) then it sounds like you're doing fine as you are.
What is the problem with your nipples - other than soreness is there any cracking/bleeding? I had awful nipple trauma with my DS so may be able to offer some advice if you can describe the pain (what it feels like, when it happens, how long it lasts) and what state your nipples are in.