I have two wifi routers. If I stand next to the main one with my laptop I can connect and access the internet no problem. The other router is in my office, and the bridging is messed up, so while I see the essid and bssid using 'iwlist scanning' and nm-tool, I can't connect to it.

Now, my main router's signal still reaches to my office, just not as strong as the borked router in my office. I need to be able to choose which wifi network to connect to without wasting time walking between rooms. I added entries for both in network-manager, but it doesn't show them in the list when I left click the tray icon! How the do I connect to the network I want?

I think you mean nm-applet list. If it won't only "desired" names it may mean that it wants to connect automaticaly. Maybe it's nic firmware. Tried to remove connection information from networks that are not shown?