Xantech makes emitters that are both IR transparent and IR opaque (get the opaque kind). I always mount the emitters over the component sensors.
...near my AV equipment...?
Which is the one you would use most of the time, presumably.
...one where my other TV is at...?
Yes you can do this, but you'd need two Xantech receivers, conn blocks, emitters for each component, and power supplies. There is another way to do it, but it adds another level (or two) of complexity and cost. It's a distribution system (that Xantech also makes).
And before anybody asks, yes, you can control two of the same device (like two Sony TVs that take the same IR codes) independently with one remote. BUT this also adds a level of complexity (cost) that most people don't want to do. You need an IR router (Xantech again) and a remote that can learn special codes. HNick