My DS had very bad rashes from his Nutramigen poops if we didn't change him immediately after he pooped. Fortunately the stench of those poops meant that we couldn't bear not to!!! LOL! Our consultant paed just said that the rashes were common on babies that were very atopic or sensitive and it was because of the way the body digests the hypoallergenic formulas and that it was not a sign of him not tolerating the formula.
We used metanium on the rashes, a VERY thin layer, it must be rubbed in so that you can see the texture of the skin through the cream. A tube lasts forever because you don't need much - it will heal the sores quickly, an overnight application is best and some of the worst rashes I've seen in DS have cleared after 24 hours with metanium. Then on TOP of the metanium a good thick layer of sudocrem as a barrier, so no more urine can get in and cause more burning. The two in combination work quickly, especially overnight, and provides some soothing relief, too!
HTH!