Depends on what you need to do, I first backed up my system with Acronis True Image, deleted the extra partitions, shrunk the Windows partition down to 40gb and then moved it to the end of the disk via Acronis Disk Director (bootable disc) (other partitioning tools should work also). Following that I created the partitions I needed before it with Disk Director but didn't format them, booted with an XP disc, went to recovery console, rebuilt the boot.ini on the windows install with bootcfg and then it was good.
Instructions for boot.ini rebuild are here, once you reboot you'll see there are two windows entries c:\boot.ini, the original will be pointing to partition 1, correct it to point to the the same partition as the newer entry and delete the new one (the original has another option other than /fastdetect on it, forget what it was now, you have to delete one, so it's quicker to correct the original by making it point to partition 3 or whatever you like.http://support.microsoft.com/kb/330184
Oh, boot.ini will likely be set read only etc. so right click "properties" uncheck "read only" so you can edit it, recheck when finished.