You can control the partition where Windows / DOS installs by hiding partitions. Many boot managers can do that on the fly, so that your Windows /DOS installation only sees the partitions you want, and that way you can also control which partition is seen as C:.

For Windows 95, 98 (and probably ME) you don't have to hide the partition, you only have to set its partition to 'active' when you install or boot it. It will then consider that partition as 'C:' and leave the DOS 6.22 files on what will then be 'D:' alone. Because if you keep the DOS partition as active and tell Windows 98 to install to D:, it will still modify the command.com etc. on C:.

Booting between the different OSes can then be done with a boot manager like Plop Boot Manager (not easy to use) or System Commander (easy to use and period correct)

Instead of installing a boot manager, you can also just toggle the "active" flag manually using any old partition manager. (Norton Ghost's "gdisk" is very convenient.) That way you don't have to worry about messing up your boot manager and rendering your computer unbootable. Or you can just use the Windows 2000 boot manager.

DOS 6.2 and Windows 98 dual boot but with Windows 2000 aswell so I can use the USB ports to transfer data.

There really isn't much point in having separate partitions for DOS 6.22 and Windows 98. There is practically nothing you can do in DOS 6.22 that you can't do just as easily in Windows 98's MS-DOS mode.

Also, Windows 98 has perfectly adequate USB support as far as data transfer is concerned and you don't need Windows 2000 for that. There are even DOS drivers for USB flash drives.