Oh man, I have been messing with my utility trailer for the past six months. I assume you are talking about this setup at ack:http://www.austinkayak.com/products/7585/Malone-TopTier-Utility-Trailer-Cross-Bar-System.html
I saw that one, but I wanted to keep my Outback below the wind behind my SUV. I also frequently tow my buddy's Outback. I also wanted to make the bars easily removeable so I could use the trailer for other purposes (deer hunting) and be able to adjust the distance the bars are apart (who knows what kayaks I will have in the future). I ended up installing unistrut bars lenghtwise down the sides of the trailer and then used unistrut fittings to affix some 3/4 galvanized pipe with pool noodles to the top of the trailer. I will admit I've had a few fails using the unistuts with the pipes moving on me. Recently I aquired some stronger pipe straps for the trailer and they seem to be holding the pipes on really well.
I have not really been a fan of the expense and overall beefiness of the kayak trailers I have seen online, which is why I went with the utility trailer.
I'd be interested to know how well the rack from Austin Kayak works if you try it. I can send you some pics of my trailer setup if you PM me. Anyone else out there have a modified utility trailer?