At present time you will have to setup weight, fuel, gpu, and general aircraft preferences over the 2D window as said on the IXEG announcement, but i am quite sure the IXEG menus will also be integrated to VR later.
Anyway, i do use their previous version (1.21) with a mod for VR and you have to only to pull up your VR headset for a minute to use the mouse over the regular monitor to set the aircraft parameters then put your vr heaset back again. You do not need to disable/enable VR or anything like that.
link to the announcement