I haven't figured out how to put them all in a single 4 track file after the fact, but it works great if you record a file in the 4x1 mode on the R-44. I've recorded with hypers on channels 1&2, and omni's on channels 3&4. In post I've mixed them 100% for channels 1&2, 75-80% channels 3&4 and they have come out sweet.
I've tried the 60%-40% mix as JD recommended, but what it does is actually lower the volume of the entire mix because your only taking 60% of this one and mixing it with only 40% of the other, so with some experimentation I've found that I've wanted 100% of the hyper recording, mixed with 75-80% of the omni's and it sounds great. This assumes that your levels aren't too hot to start out with or the resulting mix will be clipped, but it's worked out well for me.