That's a big question and there's been a ton of discussion in the forums. Its one of the primary issues shooting underwater and is dependent on a number of factors.
Indeed, if your on-camera flash is not blocked then it will indeed give you horrid backscatter, no matter where you place your external strobes. Its simple to test, just turn the external strobes off.
Posting a pic of your backscatter could help - basically if there's really large OOF (out of focus) blobs in the image, its likely a particle very close to the lens and you're somehow getting light right in front of the lens.
Of course visibility is a massive factor, with backscatter nearly impossible to avoid in mid-poor vis.
Strobe positioning is another factor, and people often point their strobes out slightly to light the subject with the edge of the beam, avoiding too much light hitting the water between the lens and subject. I started out with my strobes spaced far apart (for wide angle work) for the same reason, and much of the school of thought a few years ago was based on this principle. However, I find myself more often now keeping the strobes closer to the housing and pointing them outwards slightly. For example, if you space your strobes far out, but then have to point them inwards to light the subject, you'll still get backscatter. Granted the backscatter will be more side-lit and may not be as prominent. Its worth experimenting with and in the age of instant photo review, is easy to test in a few minutes (or perhaps worth a whole dive) UW.
Hope that helps. Cheers,
Chris