I have a really lame question. What is the best way to adjoin 2 rooms that are different sizes? Also, is there a good conveyor belt cog or a force field that allows weapons to fire through it but no passing? Or would the second question be involved in flags? Thanks

You can adjoin two sectors of different sizes if you align them so that one of the surfaces from both line up in the same plane. You can multiselect the two surfaces and press "J" to join them. JED will cleave the surfaces to make the adjoined surface. You might want to cleave the surfaces first yourself a certain way so they it's easier to align textures. There is also a plugin that will join two non-adjacent sectors by selecting two surfaces with the same number of vertices.

I'd guess your second question would deal with flags since there are different flags for weapons fire (passable) and flags for AI and player.