If you use the MS effect during recording, the mid and side inputs will get converted to a normal stereo recording before being passed to the SDHC card. Whether you record that as a stereo file or two mono files doesn't matter - it's just left and right at that point, same as if you'd recorded using a conventional stereo mic.
If you connect an MS pair to the R-44 and don't use the MS effect to record, monitoring the recording will sound weird. If you use the MS effect on playback, then it will sound ok. It's a pity that the R-44 does not allow you to hear effects during recording unless you record with effects.
If you record without the MS effect, you can vary the width on playback with the MS effect switched on, using the provided control page (see manual for details - I think it's the 'display' button). If you record with the MS effect on, you can still vary the width afterwards in a DAW using the Voxengo "MSED" VST effect (or any other that does the job). That VST effect converts the normal stereo signal you've recorded back to MS, allows you to vary the width, then converts back to normal stereo. MSED works with a stereo file, so if you've recorded two mono files you need to route them to a stereo track in your DAW and apply the effect on that track, which is marginally more complex.
Try all this thoroughly at home before using it for real.