MechJeb Ascents

First, topheavy is GOOD. Topheavy means you're stable (CoM in front of CoL). It's like a dart or paper airplane--the heavier the nose, the more stably it flies.

Now, here's how to fly an ascent with FAR/RSS (Other than turn end, this applies to Kerbin as well). With FAR, you must learn what a gravity turn actually is. Protip: it's not "fly up to 10km, pitch over 45 degrees." What a gravity turn actually is, is letting gravity pitch you over (hence its name). The way this works is that, once you reach a decent airspeed (100m/s or so, say--less if your TWR is KSP-normal rather than real-life-normal) you pitch over about five degrees and then don't touch pitch again. As gravity pulls your velocity vector downwards towards the horizon, aerodynamic forces will keep your rocket aligned with the velocity vector, and your rocket will pitch to follow. Your aim is to be horizontal at apogee.

Note that as it stands this can't actually be done with MechJeb, since MechJeb manually controls pitch all the way and keys it to altitude. However, you can set MJ to fly a decent approximation. Here are the steps.

*First, set your "turn start" to "the altitude at which you reach ~100m/s." This will be something like 1km if you have a 1.5TWR at liftoff, 1.5km if 1.2TWR, or something like 0.5km if 1.7. If you have a 2+ TWR at liftoff (from solids, say) you probably want to start your turn at 0.01km.

*Second, you want to set your "turn end" altitude and your "turn shape" such that deviation from your velocity vectory (the surface prograde indicator) is minimized. For your average two-stage rocket with a decent second-stage TWR (i.e. starts around 1, ends at maybe 3 or 4--that is, like Titan II rather than modern LVs) you might want to set turn at at 150km and turn shape at 50.

*Third, you fly a test ascent with "show ascent path" turned on. Watch how close the purple target (and your rocket's nose) is to the velocity vector. If it gets out of line by more than 5 degrees when below 80km, adjust turn end and turn shape.

*Fourth, if you find yourself circularizing after apogee (very common with low-thrust second stages), once you reach apogee you need to play with "end angle" to keep your vertical speed zeroed. Don't touch it until after apogee, mind. Then raise it until your stage is pointing vertically enough to offset gravity; as you speed up you gradually lower that angle until it reaches 0 (no up-thrust needed) at circularization.