[simplechamp]

I don't think it will make much of a difference performance wise. Using a 6S setup should help keep the current reasonable and either pack should be up to the job. I might go for the 5000mah to try and squeeze in a little extra runtime.

Many people seem to think that higher C-rating is always better, and this isn't necessarily true. Yes, you need a battery capable of producing enough current for a given setup, but once you go past that there really aren't any benefits e.g. I could use a 5000mah 50C pack, but if my system is only drawing 80A then I won't see any benefits over using a 5000mah 20C pack. I guess the exception would be voltage drop. If you are running a certain pack close to it's limits, then bumping up to the next higher C-rating would help reduce voltage drop under load. But it's always good practice to use packs that are capable of producing current beyond what your setup will draw to create a margin of safety and not overwork the packs.

The last thing I would say, and I think most will agree, is that C-ratings can vary greatly. Some people say brand X overrates their packs extremely, and others swear brand Y packs can produce far more than their rated current without extreme voltage drop. Again, the best bet is to assume any pack is slightly overrated, and plan for it buy using packs that can perform above and beyond what your setup will draw from them.