Just like Ako showed you, if you are only using a single crystal.
When using multiple, you need tubes and retrievers. Sadly I am not at my computer, so no ability for screenshots via dropbox. Text will have to do.
You'll need a 3x3 area. In one corner (let's say southeast corner), place the ender chest. On the west side of the enderchest, place a filter (RP2 item) and configure it to only transfer full energy crystals. On the north side of the enderchest, place a retriever (RP2 item) and configure it to only transfer empty energy crystals. Make sure the filter is rotated to pump out of the enderchest (small hole facing away) and the retriever is rotated to pump into the enderchest (small hole towards the chest). Now place pneumatic tubes (RP2 item) from the output of the filter to the input of the retriever. You should need 5 tubes and end up with the tubes and the 3 devices occupying the entire outer ring of the 3x3 area, leaving only the center block free. Now place a timer (RP2 item) into that center block, so that it faces towards the filter or the retriever (either works, as the timer will also pulse towards the side to reach the other machine).
The retriever needs blutricity to run. The easiest way to supply it is placing a RP2 solar panel directly on top of it, provided it can see the sky (same rules as IC2 solar panels). The retriever needs more than 60% internal energy storage filled before it can start working, so the single panel will take a while to get there, but once past that mark it will work. The retriever uses so little energy per operation that the single panel will easily keep it working forever.
Now you can place your batbox/MFE/MFSU anywhere on top of the 5 sections of pneumatic tube you put down. The location doesn't matter, it works anywhere. It even works if you place multiple ones.
And the last order of business is placing some filled energy crystals into the enderchest, obviously.
On each timer pulse, the filter will attempt to send a full crystal out of the enderchest and into the pipe (but only succeed if there is a valid destination, i.e. the batbox/MFE/MFSU bottom slot is empty). Also on each timer pulse, the retriever will attempt to pull an empty crystal towards itself (but will only succeed if there is an empty crystal to be pulled), and through itself, send it into the enderchest.