Tim,
So many options! Each composition or goal would necessitate it's own special requirements. But in general:
For close macro work one technique would be to position the main strobe just above the lens, aiming downward at an angle. The fill strobe would be set to the side, aiming in towards the composition. In macro work backscatter is not as much an issue so illuminating the water column between the lens and the target is an acceptable practice.
It was explained to me is that the position of the main strobe in the previous example recreates where one might assume the Sun to be naturally positioned in the sky. The responsibility of the fill strobe would be to minimize (not eliminate!) the shadows created by the main strobe. Shadows do create depth and therefore a three dimensional feeling to the composition. It is best not to eliminate shadows completely.
In this example the power level of the fill strobe is less than that of the main. This could be accomplished either by a manual intensity level setting on the strobe or by strobe to subject distance. As a guide, for every foot of water strobe light has to penetrate (from strobe to subject), an f/stop of intensity is filtered out. Both strobes therefore could be set to equal intensity but if one was further away from the subject, it's influence would be diminished.
An alternative approach for illuminating macro work may be to position the strobes equidistant on either side of the lens, again varying their intensity to avoid a "flat" image.
Chris Bangs has an excellent tutorial started here. Anyone reading this post should take the time to go back to the beginning of the thread. Another source of information I would recommend comes from Chris Simmons:
http://www.kelpfish.net/strobe.html
regards,
b