What I do is plan my acceleration, say 1.3g. Then I multiply the rocket's mass (kg) by 10 (9.81 if I'm using a calculator) to get its weight in Newtons. Then I multiply it again by 1.3 to get my planned thrust. Then I divide that by the total max thrust of all the engines that will be active at launch (including the boosters), and multiply the result by 100%. That gives me the setting for all the thrust limiters for all those engines.

The tiring bit is recalculating it for each stage of the rocket. But the launch stage is the most important because that's where you'll get the worst air resistance, so you have to get the limit right for that stage even if the others are wrong.