Board Thread:Questions and Answers/@comment-74.190.39.37-20121219020522/@comment-212.159.121.228-20130114135822

Make sure you're using the right pump, its almost certainly the buildcraft pump you want, and the waterproof pipe can go in any face.

Alternatively you may be using lava cells or buckets in which case its definitely the bottom face. A lava-bucket system requires a retriever and blutricity to remove the empty bucket.