The best way to do this is to use a sacrificial board with alignment marks.
This could be a piece of thick card, we use white poster board, or a flat piece of 5-10mm wood. Make sure the board is at least A4 or A3 in size, depending on the Emblaser you have.
Tape it down onto your base plate so it doesn't move around The reason it is called a 'sacrificial board', is that it will get scored, burnt, marked and ultimately need replacing, instead of your machine base plate.
You can now 'home' your machine and 'burn a grid onto it, or better still, an outline of your object to be engraved / cut. This way you can use it for perfect alignment.
You can find some useful files for alignment and testing here: Link