Ok lots of question which is good.
The machine will home on startup(machine origin)
Using the jog function on the display, move your x and y postion to create your work origin (0,0) I use a vbit and tape on the work material to locate that spot accurately. This is where the machine knows as centre (if you chose centre of the workpiece as your datum) (See pictures in the bottom of linked post)
As for aligning your piece first make sure your clamps can reach the piece (4 clamps if possible to be safe) In order to align to the spoilboard I manually cut a 1/16" deep v groove into the spoilboard in both X and Y positions. This ensures your work piece is parallel to the machine regardless of the clamps and t-tracks.
So the software asks for a size, think of it as canvas for a painting (generally you don’t go all the way to edges on a design- so if your canvas is 8x8 (Maximum size) and your design is 6x6 in the middle then no problem hitting clamps
If you work from centre (initially) you avoid offsets and indexing. Once you have mastered the basics then go to more advanced setups
Depth of cut- start small 0.0625 per pass- feel the machine 0.25 is too aggressive for a first cut
If the piece you are using is .75 thick you want your depth of cut to be .745 or use tabs on the edges. I rarely ever cut into my spoilboard 1. because it leaves and uneven surface and 2,- the remaining “onion skin” at the bottom holds the work piece from breaking free and being damaged by the spinning bit
Looking at your G-Code- remember to always have your work blank bigger than your project piece and always do the perimeter cutting last
Here’s a link on homing and setting up a work origin (the pictures are near the bottom of the post and its for the Masso but the process is the same.