MechJeb doesn't recognize the RealChute parachutes and it's very sad indeed, considering how powerful that tool really is.

With latest changes in RC fine tuning, basic integration seems to be quite simple:

1. Make MJ aware of RC parts onboard as it is aware of stock chutes.
2. Make Landing Guidance to stop burning when reaching mid-air periapsis (instead of standard landcrashing course) then "Arm Parachute" for all RC parts on the closest stage right before atmospheric reentry.
3. To save fuel - stop engines until final landing stage - few meters above ground. Just use RCS or reaction wheels to stop spinning and help chutes keep retrograde.
4. Detect "Autocut" while descending. If all active chutes (except combo chutes!) are cut and vessel still not landed - repeat part 2. If there are no more avaiable chutes (remember that combos have TWO) - activate standard landing procedure.
5. When few meters above ground - activate engines and perform standard soft landing routine.

Of course it is the most basic integration, not even slightly close to targetted landing, but it's much better than nothing.