I screw my work down to the table and I normally keep a safe z height of 2" to avoid any problems.
When I work with sheet stock, I program a drilling toolpath to put a small divot in the sheet where screws can be located. Small parts are held in with tabs and large parts the sawdust from the cuts keeps them secure.
When putting in a screw, drive the screw home then back it out from the base material. Then put pressure on the screw and it should pull tight to the waist board.
So far this method has saved me a ton of cash! I don't have to make a vacuum table!
http://www.glenspeymillworks.com Techno LC4896 - 2.2Kw Water Cooled Spindle | Moving Table Mill from Omis 3 CMM, 500Lb granite base | Epilog Legend 32 Laser Engraver