I am gonna put a 3000 watt peak inverter in my van
You gonna run an 8" Makita and a microwave at the same time?
I think my idea will work I will run a positive wire back to my deep cycle in the cube,
Make sure you fuse it right before it hits the battery. A good ANL can be used, a Class-T is preferred. Use thicker wire than might be indicated for the current load, to minimize the voltage drop that occurs for longer cables. 10 feet of cable can be as much as half a volt drop, depending on the size cable that's used. If the alternator is putting out 13.5 volts and .5 of that is lost in the cable, then only 13 volts are gonna get to the bank, which won't charge it.
Should be a battery isolator, or a battery separator if your alternator doesn't get along with and play well with isolators. A simple switch will get you into trouble because you
will forget to switch it, thereby running the cranking battery down. Get an isolator by Sure Power or Hеllroaring.
run 2 heavy wires to inverter,
Again, fuse the positive cable right before it connects to the battery.
If you're going to run any other 12-volt loads off the batteries (Espar, roof vent fan, Igloo cooler or other 12-volt appliances), you should consider a busbar for those connections, rather than a snotload of 12-volt connections to the battery terminals.
and then ground through a hole i will drill down under the cube.
You don't need to go all the way down to the ground. You can just ground it on the chassis.
anyone think my idea will work ?
Sure. If you know a local RV repair guy, might want to run the installation details by him, as well.