Mining instructions on front page have been change so that by default you do NOT support merged mining.
To NOT support merge mining, make sure your source code is on the same version with:
git checkout 0fd82c910b8e4cbf0b3940d6e42f2e992287582d
To support merge mining, change your source code to master with
git checkout master
TFT has said he will add an explicit voting option, and that votes before it is added won't count:
That's right. Results will be calculated starting from the moment an explicit voting option will be provided.