To address your points one at a time:
If you want to combine the space on your 5GB and 20GB drives, the only way to do this is using LVM (Logical Volume Management), which is included with Fedora. Unfortunately to convert from a conventional partitioned disk to LVM requires a complete reformat of both disks.
To configure Linux as a dual boot system, for example with Windows, the bootloader must be the Linux bootloader, and must be installed on the master boot sector. Using the Linux boot loader, you can then choose to boot to Linux or Windows (or whatever your "other" OS is).
I would say your best bet is a complete reinstall. From a partitioning point of view, there isn't much point allocating a separate partition to /usr, you'd be better off allocating the space to /home as this is where user profiles are stored.
Just a question - why are you installing FC3, which is well over a year old, rather than FC4, which is more recent, or even FC5 which came out a few months ago?