what exactly is it you want to do? are you resizing the windows (either system or data) partition(s), or changing free space to or from linux partitions?
anything to do with resizing windows partitions is a bit iffy. if FAT, defrag everything to the front of the drive before shrinking it, enlarging *should* be fine (but don't trust me, or win). NTFS, i have no idea. best doing this from within win (if you can).
if you're doing anything else, like deleting old/unused linux partitions (ie making free space), windows won't have a problem with that.
making new partitions is fine for anything, as long as it's already free space (see above). if you're making a new partition for win, best do it inside win (my win2000pro has a nice partitioner on it, dunno what you're using though)