This may seem like a dumb question, but what order should I assemble my box?

Should the top piece be the last on so that bracing can be added easily and all bottom edges sealed?

If this is so, how do I seal the edge behind the port on the topside?

Is any silicon sealant ok to use?

Also should i cut the sub holes into the baffle first or last?

 

1) For a box like that, yes I often put the top or bottom on last.

2) Doesn't really need it. The bead of woodglue on top should be fine. If it makes you feel better, silicone the front side of that joint through the woofer hole.

3) Pretty much. I buy whatever is on sale - usually something Latex based for easy cleanup.

4) I like to cut it first. Then you don't have to vacuum out the box.