Firstly, execute the BSP conversion itself (using Entity).
Secondly, build a new sky, or use Gemin's sky. I'l be using scenarios\skies\solo\earthcity\bridge_sky.
Open your Gemini in Entity. Navigate to the [Scrn] tag, right click>idents.

Find the [Sky] ident, (there should be two) Select the first. Right click>clone chunk.

Find the same [Sky] reflexive in the chunk cloner. Input the number 5 in the clone box. And hit "clone".

This is what you should see afterwards, hit "add meta to map".

Navigate once more to the [Scrn] tag. Right click>idents. There now should be six [Sky] chunks. Null all of them out except chunk number four, that is the one you will see in-game. Swap the [Sky] chunk number four with the sky of your choice.

That's it. If all went well you should have gone from this:

To this (minus the Scarab and other items):

Credit goes to The Swamp Fox for leaving his Gate mod unlocked, or else I would'nt have been able to learn from it.