Downsizing to smaller rig, battery capacity

Have no idea what you mean by "standard size batteries". Deep cycle 12 volt batteries are Group 24, Group 27, Group 31, sometimes also a Group 29. The greater the Group number the larger the battery is but also the greater is it's capacity. Since a CPAP draws quite a bit of power, especially if you need it's humidifier running also, I'd go with the larger Group 31 if there's sufficient space to mount them. Otherwise you might want to switch to a pair of 6 volt GC-2 batteries which in series will offer about the same capacity as a pair of Group 31 12 volt batteries wired in parallel, and although taller will have a much smaller footprint, about the same as a Group 24 12 volt battery.