Bi-amping through the factory passive crossovers typically yields minimal improvements. Identical amps must be used with this configuration.
To correctly use active crossovers the factory passive crossovers must be bypassed. Furthermore, whatever other filters existing in the factory passive crossovers (baffle step, zobel, etc.) must be duplicated in the active crossover. The type of crossover filters (first order, second order,
Butterworth, Linkwitz-Riley, etc.) should be duplicated or the response and phase can be altered in a very negative way.
While many believe using active crossovers have many benefits (and they do) just swapping out the factory passive crossovers for active crossovers does not guaranty better results. You might get lucky. Building active crossovers that are correct for the speakers and drivers will.
Duplicating the passive Magnepan crossovers in your active crossovers is the right way otherwise you are designing your own speakers. Digital crossovers (DSP) work great as long as you know what you are doing. Maybe a Magnepan person can share the 3.5r crossover specs so you know what needs to be duplicated.
Designing and manufacturing speaker system, we have tried passive, analog active and digital (DSP) active on the same speakers. They all have their pros and cons. Digital crossovers usually win, as long as you use a good quality DSP.
Read as much as you can about active crossovers before you make your decision. There is much written on the subject.
https://www.marchandelec.com/xm9-electronic-crossover.htmlhttps://www.xkitz.com/