It sounds like you've built the smallest TP room (1x2 squares), which only allows one beacon to be placed. You'll need to either add a second small room, or upgrade to the next size up (2x2) in order to add extra beacons.
A second small room will be cheaper in the short term, but you'd need to build a second teleporter. The 2x2 room costs an extra 100,000 prestige IIRC, but can hold 2 teleporters, and up to 4 beacons. The real challenge comes with arranging these without blocking doors!
I put my first base together last night, which was all going ok(ish), until I tried to put the second beacon in my teleporter, what am I not doing , or what should I have done ??
@Boy Wonder
Quantum Flash - Ill/Kin Controller
Leader of the Legion of Heroes