Is there a certain way you have to take pictures (ie custom settings)? Or can you just go about like you are using a normal camera and keep the regular settings?
With a modified camera, your settings are, more or less, the same as if you were shooting with an un-modified camera. You have to be careful of exposure though as what you think would be a proper exposure using visible light may either under or over expose you shot in IR. It's best to keep a close watch on the histogram.
Something else that REALLY makes the post processing much easier is to shoot in RAW. Correcting the WB in RAW is so much easier than when working with a JPG (plus you have more data to work with).