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if my primarly partion messes up and i have to reformat does my secondary partion get reformated also?
can i still transfer my stuff to the new partion ?? without having an OS on my secondary? >>
ehrm...
ok..if you ask such questions i'd highly recommend stay away from ANY partitioning

(I dont mean it in a bad way)
I spent the last 2 days setting up a dual boot (XP <> 98) and moving around partitions with PartitionMagic Pro7.0/ Multiple primaries/Partition hiding etc...and it was a pain in the a$$...not necessareliy something i want to do every day...
If you really HAVE TO deal with partitions..then please ONLY with partitionmagic....anyway i still wont recommend doing it if you're not at least familiar with the basics..eg. formatting partitions etc....
* You need only ONE OS of course....on C:.... you can have OTHER partitions/drives.....D:, E:, F:.....you do not need an OS on them to access the data.
The partitions then are available as logical drives..eg. you have 98 on C:, and then it looks like you have some more drives D:, E:, whatever...depending on how many partitions you created.
===== SNIP ===========
Win9x/ME will only install on the first FAT formatted partition on the system.
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hehehe...that's not true

With PartitionMagic you can create multiple primaries, set them active and hide another.
I have my 98/SE partition (since i switched to XP Pro) back on the END of the HD....it's a primary drive C: <--- on the very end
When i activate the FIRST (XP) partition (and HIDE the other C: )...then the partition at the beginning of my HD gets active and becomes "C:" <--- this is my fast partition in the front which is for XP

)
Anyway partiton hiding and related is (afaik) only supported by partitionmagic/pqboot and some boot managers....FDISK tho does ACTIVATE a desired partition, but it does not HIDE the other one...so you NEED some more advanced tools...mandatory.....glad i got PM7.0.
Edit:
if you format a drive/partition C: then of course it doesnt affect your E: or D:, it's almost like having separate harddisks...the main purpose of having more partitions. For doing backups....and in case one partition gets hosed you have a backup on the other....or multiple OS on different partitions etc.....getting everything a bit more organized instead of having all on ONE big big partition.
I always have one around 12 gig partition on the very end of my HD (slower than in front) which is a storage/backup partition with stuff which usually isnt accesed all the time.
I'd recommend (i do, idont know about other setups) like a 3 gig partition C: on front for the 98/SE system (4gig for XP), then a bigger (15/20Gig or so) partition D: with all your programs and Data....and the last partition like 10gig for storage and backup. (More partitions for things like multi boot/multi OS etc...)
greets