If you're doing a double sided design where symmetry is important, be sure to do a horizontal flip before printing in Corel Draw to make sure things line up. I learned this the hard way working on the Enyo ornaments.
When you do your test run, look for overdraws and edit those out using the Corel object editor. Auto-trace can often leave these in, and they just end up causing longer jobs and scorching.
When you're mixing engraving and cutting, make the engraved bitmap the black color. For some reason, Trotec's software just wasn't seeing non-grayscale as something that could be etched, even though Job Control allows setting that up. It's OK to use lots of colors for all your cutting layers.
When possible, use multiple colors for your vectors to order cuts. This is important if you're cutting small features out of larger shapes and using plywood that has a tendency to be uneven, so if you cut the larger features first, you may be out of focus for the interior ones if the work material has dropped.
Always use the job estimation feature in Job Control. Not only does it show about how long the laser will take, but it lets you know quickly if the software isn't understanding your layers.