Personally, I exclusively use Illustrator CS6 for everything.
The laser software doesn't seen to recognise colours from illustrator (except for the odd grey here and there) so just stroke everything in black.
Also, don't use fills - it wont recognise them. Simply stroke everything with an empty fill (not white etc). I tend to use a 0.01mm stroke width as I can see fine detail with that size if needed.
You can group objects together in Illustrator but the laser software won't see more than 2 levels deep of groups - I usually ungroup everything individually and then group as one for final export.
If you want to grade engrave or the like then make sure you have a bounding box around your item to be engraved so the laser knows it is to be engraved within that area (as a pointer - create another bounding box 2mm smaller and use this as the 'cut' line as a grade engrave ramps up at the edges).
Forget layering in Illustrator - I pay no attention to them when designing for the laser.
Export to dxf via the export dialogue and ensure the top 'version' drop down menu is set to R14, you can leave all other options as they are (unless you have artwork selected and you only want to export the selected artwork, then tick the relevant box).
Hope that helps a little.
Mark