I keep reading this hoping that it will make sense. So perhaps an example will help me make sense of it. Assuming a size 6 engine with 1MSP dedicated to warhead, how big should my engine and my fuel be for your formula?
Basically, you allocate a certain amount of propulsion space on the missile (P) which is equal to engine space (E) + fuel space (F). For the best speed/range (one is maximized while the other is fixed) E= .7609*P and F= .2391*P. So if you're allocating P=6, then E=4.57 and F=1.43.
The one caveat is that this assumes there is no cap on the power multiplier you can use. You may very well need more engine than these numbers would indicate, particularly for things like AMMs. The most important rule is that you shouldn't have a missile that doesn't have max-size engines and has more than a third of the engine space in fuel.
What do you put on your decoys? I've never played with multi stage missle designs before, but that sounds interesting.
My basic missiles are all size 1, and I have the tech to make this work. (In fairness, I was as concerned with getting missiles through really heavy defenses as I was with raw damage, which may not have been the absolute optimum.) The standard missile does about 150,000 km/s, and has a size-4 warhead with a range of 17 mkm, IIRC. I mount from 1 to 3 of them on a size 4 bus which has a much more efficient and less powerful engine, and then fire them at targets at ranges up to around 1,000 mkm. The bus doesn't need to go fast as it doesn't have to get through defenses. Each stage can be optimized for its own job. The decoys are set up to be very slightly faster than the actual warhead missiles, and are released at the same time. Each fire control has one tube of decoys and usually about 5 tubes of regular missiles. The decoys separate at the same time, and double the number of different targets, which helps saturate fire control on the receiving end. They're also a bit ahead of the regular missiles, so they get shot at first. As the difference in speed is usually 100 km/s, they normally arrive on the same increment as the attack missiles, and draw off all the beam PD.
The decoys have a slightly different (more powerful) engine than the regular missiles, fuel to have the same range, and everything else is armor.
Can't have too many things at once fixed.
If E is engine tonnage, S is size of the missile, A is Agility points per MSP.
Ideal fuel is 0.4E if using maximum-size engines already, 0.3182*E otherwise.
Ideal agility to maximise to hit chance on a given budget for engine and agility is E-10S/A (this requires fine-tuning to avoid losses to rounding, and ignores possible fuel savings by larger engines).
Subbing numbers for a size 6 missile with 1 MSP warhead (which I assume you meant), we put in the numbers of non-warhead space of 5:
5=2.3182E-60/A
If you have a missile agility tech of 80:
5=2.3182E-0.75, for an engine size of 2.4803, and corresponding fuel of 0.7892 and agility of 1.7304 with 1/10000 of a MSP lost in rounding
We don't care, as agility will need some adjusting to avoid rounding losses.
Something seems off with your math. I can't see where that equation comes from, and I definitely don't see a factor for engine power per MSP in there, which would be an important part of the trade. In some cases, making the missile faster is better than adding agility, because it has other benefits, too.
In practice, this beautiful precision is unnecessary to counterproductive as there may be other considerations:
I never have enough engine multiplier tech to hit the ideal without excessive range (if I do, I messed up research priorities).
This is pretty common, particularly for AMMs.
Also, bigger lower-power engine and less fuel is cheaper.
I'm not so sure about this. I may have to play with numbers.
I usually want more engine and less agility than the theoretical optimum: faster to better evade PD, better range for free if we can increase engine size, and again usually cheaper.
This I will agree with. My second stages have no agility at all, while the AMMs use the same engine and have a smaller warhead.
In practice, 40% engines, 30% warhead+sensors, 20% agility, 10% fuel is my guideline for general-purpose missiles. If you're set on a different payload, the 4:2:1 ratio of engine to agility to fuel remains useful.
That's going to give you about 95% of the efficiency of a proper optimum. Which is decent, but not perfect.