Cut2D doesn't support tool changes.
If you have a look at the vectric forums there have been a couple of people talk about workarounds for this.
In my case what I did was:
Use the same tool number for all your tools in Cut2D.
Create each tool path in the order you want, and add a single drill tool path to a known point in between each one.
Select all visible tool paths, export them to a .tap file.
Edit the .tap file in a text editor searching for the known X/Y co-ordinates of the drill path and the replace the drill path with the pause or tool change code for your machine as appropriate.
I did this for a series of roughing / finishing / engraving cuts using three tools and it worked quite well for what I wanted.
I've now upgraded to vCarvePro and haven't actually tried a multi-tool job yet, I must give it a go and see what happens.... I'm currently using EMC, so I assume it supports tool changes, but dunno what it would do. :-)
Cheers, Chris H.