I am trying to create virtual AP, and to be managed by capsman, while keep physical interface wlan1 and wlan2 as it is. Would this possible?
It's on Mikroitk hAP AC2. so far I've not managed to do it.
PS: Capsman config is correct and I have mutiple Mikrotik CAP AC devices managed by it.

I doubt you can use the virtual without the master interface being part of capsman.
Even disabling master will instantly disable slave connected to it as well.

This is not possible, you hand over control to capsman on a per-(physical-)interface basis.