Download the mapping files from the gemini site.
There are 4 different mappings, 1 for each traktor deck.
Import all 4 in to traktor.
Leave the ports as all ports for each file but set the focus to deck 1, deck 2, deck 3, and deck 4 respectively.
Then on the CDJ's enter midi mode. Hold the MIDI button down for a few seconds.
Then hit hot cue 1 if you want to control traktor deck 1, HC2 if you want deck 2, HC3 for deck 3 and Memo for deck 4.
If you are still having issues, try using a USB hub or better usb cables.

with the audio.. On a mac search audio midi settings. Make a new aggregate device with both CDJ's and use that as the sound card. in traktor with external mixing. if you're on a PC download gemini's ASIO soundcard and use that as the soundcard. It'll lower your audio latency significantly.