Biesse Rover S FT - NEED HELP PLEASE

Hey, this is going to be a very basic question for some of you out there but just to provide context. I'm doing a cabinet making apprenticeship and am now running our Biesse Rover S FT as well as our CNC operator left. I have no proper training on the machine and am completely learning as I go and by myself.

I want to know the following:

1.) How do I change the layout of pieces after they have been nested to ensure there is no mini offcuts that lose vacuum and get caught as the machine is passing/damage the tool as it's making a pass.
2.) Currently, my tool is going too deep and also milling and boring into my cnc board while it's running the program, how do I raise this or ensure this doesnt happen, as it is causing problems with dust and I will go through my CNC board way quicker.

Thank you!

Hi, how do you make programs, in Biesse works or something else?
Sorry, I don't understand the first question - do you want to edit the program?
The answer for second question is to set correct thickness of MDF support (jig thickness), which is usually in program or there is used dynamic jig thickness on Biesse machines, which is possible to change by pressing button "jig thickness" on console when machine is in Manual movements.

have you solved your problem?
what kind of Software and version? (Bsuite/Bsolid?