I also like to use a gear indicator on all my bikes. Last year, I upgraded to a 6700 rear shifter on one of my bikes and faced this same dilemma. I wrote about it in a thread somewhere on BF, and the only useful response was from someone who had mounted the indicator along the handlebar, between the stem and where the cable exited the bar tape. I sometimes use clip-on aerobars, so this wouldn't work for me. I instead elected to put it just before the cable stop on the down tube. This functioned OK, but the location was far from ideal. After about 6-9 months, the plastic surround of the indicator broke where the cable housing entered it because when the bars turned, it put pressure on this plastic. I've now removed it and it is now the only bike I use without a gear indicator. I find that looking back at the cassette is equally as easy as was looking down at the gear indicator when mounted on the down-tube.

I'd still prefer to have a gear indicator in the traditional position, somewhere near the front of the shifter/brake lever, but this doesn't seem possible with the under-the-bar-tape levers. Near the stem might work for you, but I wouldn't bother if you have to put it near the down-tube.