You never want to start out at low thrust:
You want to full burn up to some point (We figure it's a bit above 200m/s)
then throttle down(still gaining speed) to some undetermined point, and slowly throttle up.
Many vehicles can burn at full thrust all the way, depending on the thrust/weight ration, so this might not apply to your craft.
to the new guys, go read wikipedia on gravity drag, and you will see why.
Actually, we have those science sensors now! They tell atmospheric pressure, g forces, and the force of gravity. I suspect with some decent calculus, we might actually get to the bottom of the exact numbers. In any case, vaccuum appears to start at ~45km; so anything above there should always be as full thrust as is practical.
As for atmospheric pressure, it appears to be about 50% the starting pressure at around 3500m, droping to 33% at around 5500m, 20% at 8000m, 10% at 11000m, 5% at 15000m, 1% at 23000, 0.1% at 35000.
The air resistance should be proportional to the density of the air. That density is generally hard to calculate, and as such, I will assume KSP has a simple system where the two are effectively one and the same (if they simulate air temperature in the atmosphere somehow, this is a false assumption; but I'm pretty sure they don't actually do that). Which in turn means that, ignoring staging, air resistance force is relative to those values above. The other thing of note in the drag formula is that it uses velocity squared. Doubling velocity quadruples air resistance. Though doubling velocity also causes air density to drop off at the measured rates much more quickly, as well as reducing the delta v lost to gravity. So it's mostly a matter of balancing a few integrals. !!SCIENCE!!