I used to use system commander for trying out OSes. I had windows 98, 2000, XP and about 10 differnent linux distros. There's pretty good instructions on the website for installing different OSes, but I had a hard time using the wizards to set them up. Easier to create the partitions manually then install the os and boot into it. The version I was using (7.05) did not have support for formatting newer file systems either such as Ext3 or Reiserfs - This is something I found that I had to do during the actual installation of Linux.
If you only want to install one version of windows and one or more versions of linux, it's actually much easier to use the bootloaders that come with linux, either lilo or grub.
My 2 cents, use lilo or grub unless you want to try some really weird setup or strange OSes.
If you do want to carry on using it though, post your specific problem.
Cheers
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