I would use the sound desk. It's always on & you won't need to swap it out every couple weeks. Hopefully... :)
Drawbacks? You may need to use a ground lift on your keyboard if there's hum. For a relatively stationary system like a church...no need to fiddle with batteries.
To which input should I insert both an active di-box with a passive
guitar and a passive dibox with an active guitar?
MIC input without phantom power (unless the active DI box is powered by phantom power).
To which inputs should I insert all the rest of the guitars without
di-box and different types of the pickups?
How can my 3-4 ...
1. "Can I feed DI box output into the line inputs in my mixer?"
Your typical Behringer mixer has a gain range of -10 to +40 dB with the line in, but this varies from mixer to mixer (look it up in the specs section of the manual).
The signal level from the DI box greatly depends on what you connect to it and the DI box model. But generally you get ranges ...