When starting out be sure to mill the top of your CNC machine so that it is perfectly flat. This makes z-measurements more accurate across the table for larger pieces. It also produces a small lip around edge which is useful for using spacer blocks to setup/align material to be clamped so that it is perfectly alined with the x or y axis (it also helps visualize the working space available). Another thing you may want to do is v-carve a grid across the workspace to help with aligning material.