Hello matt.newman, For the MD1000 you can swap a failed drive while the MD1000 is running.  When the replacement drive is inserted it will start a rebuild.  For replacing the Perc6 what you will need to do is the following: Please let us know if you have any other questions.
What would prevent me from wanting to do a Hot Swap on a 136GB 15K SAS drive in an MD1000 PowerVault with a PERC 6/E controller set for Adaptive Read Ahead, Write back policy, 64KB stripe, disabled Disk cache policy, RAID-10 in degraded state, one failed disk? Blew a drive and want to make sure I can hot swap on this machine. I read through product docs, but am looking for anything additional I may want to check I missed on. Server our of warranty and support as of last year. Everything I see was green lit to go, but I would always like to get as many resources going as possible before potentially blowing a RAID 10 because a controller had some one off setting that prevented a good hot swap to rebuild. Doing backups before swap, doing swap during off peak hours so rebuild doesn't commence on business operations.   I have read through docs: [URL] [URL] [URL]     
MD1000 PowerVault Hot swap Perc 6/E