you need tram to the table. your workpiece is not a reference surface. I'm not familair with that mill, but if there is not an adjustment in that direction, its a problem - shims maybe?
Do you have an indicator? The usuall approach is to get the spindle axis square to the table by holding indicator on some sort of extension arm in the mill spindle. When the mill is correctly trammed you will see the cicle of the flycut, the cirlces start overlapping and you get the cross-hatch pattern.
How deep to cut depends, on the mill, material, cutter. what dia is the fly cutter? Since a flycutter is a larger dia cutter, depth of cut is less than for other cutters as this cutter has more leverage on the spindle. at somepoint, the mill runs out of hp but it should handle a lot more than a thou. Also, don't forget to work out your cutting speed.