What I find helpful when designing missiles under the new system is to design a junk 0.1 engine at max power value, then using that as a guide for the final design of the engine. For instance, designing a size 4 shipkiller, I start at size 1 warhead, .5 fuel, and .5 agility. Then, I size up my engine, and get to adjusting fuel, engine, and agility until I'm happy with what I got(keeping in mind that the final range of the missile is gonna be much greater with a purpose-built engine for the missile, due to larger missile engines being more fuel efficient). The only time when I break this process is designing missile busses, since it would be a max size engine anyways, the only variable is power, trading off wether I want a faster, shorter ranged missile, or a slower, longer ranged missile. Currently, for my Minuteman ISBMs, I'm using a 3x power booster engine, wich gets decent speed while still having a LOT of range, even when carrying 6 of my size 2 Exocets!
Personally, my algorithm is to figure out what size payload (warhead, sensors and stuff) I want to put in what size missile, and then allocate 1/2 of the free space to engines in an AMM, 3/4 to engine in an anti-FAC missile, and all of it to engine in an ASM, a bus or a sensor drone, and then taking the fuel out of the Agility budget. Under the new missile design rules fuel budgets get comparatively trivial as long as you make decently sized anti-ship missiles, so this is not a bad approximation.
