1 - Rockbox already comes with the appropriate stock battery capacity selected by default.
2 - The "charge" reading, in terms of percentage, is not affected by the battery capacity setting - only the calculated runtime (if your WPS displays it).
3 - The calculated runtime is not very accurate on iPods (all PP?), and the inaccuracy varies depending on usage pattern. It is better, IMHO, to tweak the capacity setting (lying to Rockbox as it were) until you get an estimated runtime closer to that you actually experience.