While I'm not the biggest fan of the separate entrance/exits, they are being marked quiet easily for guests. Unlike Diagon, it'll be easy to see where you're supposed to enter and exit.
Out of all the portals, the SNW is the easiest to navigate due to the land's multi-level construction. You will essentially be lifted towards the 2nd level as you enter, and then have to drop to the lower levels for the attractions, shops, etc. Once your done, just walk out. Not that hard.
Regarding Virtual Queue, I'd imagine it will be temporary and only utilized during busier periods. I could see a scenario where VL will be required for your first land entry (to spread out crowds) and then allow access everywhere else after. Kind of like how Disney requires you to tap in to your first park before park hopping.