BetterTouchTool does not support two finger tap/click actions. There was an experimental version a long time ago but it was implemented in a 'hacky' way and never really worked right.
BetterTouchTool does let you set up a TipTap to middle click, so that you can press with a second finger whilst your first is down (sort of like a two finger click but with a delay) to activate a middle click:
Alternatively, you can set up a tap/press with three fingers to middle click in BetterTouchTool. This is supported fine:
If you're really looking for a two-finger click, KeyRemap4MacBook lets you remap right click to middle click using a private.xml such as this:
<name>Right Click to Middle Click</name>
See private.xml documentation for more information and to limit to certain apps.