I asked a very similar question a while back. Have a read of this thread:

Multi Boot Dos 6.22, Windows 98 SE and Windows XP Pro

You'd be better off just installing Windows 98SE though as it contains Dos 7 already. I haven't run into compatibility issues yet using Dos 7 as opposed to Dos 6.22. A lot easier this way and if you want to have boot options at startup then have a read of this:

http://ozzyfrank.150m.com/pages/pc/Windows/msdos_sys.htm

Hi, well my method appears to be working. I installed DOS first, then installed Win98 from the CD, setting the install location to D:/WINDOWS/ (where D is my FAT32 partition). In the advanced startup options I checked "enable boot menu" and then when rebooting, selected option 7, the "Previous DOS installation" and it worked fine, swapping out the autoexec.dos & config.dos files as it should do.

Remember to ask questions about old hardware and how to set it up in Marvin. This forum is for DOS games.

http://www.mdgx.com/osr2.htm#2BOOT

"DUAL-BOOT IN OSR2/WIN98

Under Windows 95B/95C OSR 2.x or 98/98 SE(U) you can boot to the previous MS-DOS version 6.xx for only ONE (1) time, after which you'll find impossible to boot back to OSR2/Win98, UNLESS you apply one of these "patches"!"

The best way IMO would be to use a primary 2GB FAT16 partition and a 38GB FAT32 partition (you can have up to 4 primary partitions). Then you can use an additional boot manager which will install itself into the MBR.

Using the W98 boot option is restricted to only one DOS version and W98, and it needs to swap out the files on the hard disk (probably not only autoexec and config, but also io.sys and msdos.sys). I suppose that option was meant for trouble shooting. Advantage is that it works with only one partition, as long as that's FAT16.

^^ agree with borgie83. MS-DOS mode of Windows 98SE does everything you need.

1) MSDOS 6.22 not supports FAT32 at all.
2) Win95B/95C/98/98SE can't boot from the FAT16 partition. Well, they can, but the partition info will be broken after the 1 boot.
So - use MSDOS 7.0 or 3rd party boot managers.
3) Micro$oft - doing it wrong since 199x...

Thread resurrection, apologies. I ran into this issue and when using DOS 7.x, some applications identify it as running Win9x and thus won’t complete the install process.

As mentioned above, creating multiple primary partitions and then installing a 3rd party boot loader into the MBR is probably the way to go.

I tend to use IDE2CF adapters but I haven’t tried petitioning like that beyond an 8gb card for anything DOS 6.22 related. Unfortunately I’ve packed up all of my retro pc equipment as I’m preparing to move, but once I’m all set up at the new house my first order of business will be sorting out the best method to use, as well as SMB network sharing in DOS 6.22 using a custom NAS, nothing off the shelf.

If you are already using a boot manager (say grub4dos) you don't have to install Windows on "letter" D: (which is another compatibility nightmare) , and you don't need to have only one visible primary partition.
Just boot from the desired partition's boot record.
As far as I can see, on win9x the partition you're booting from always becomes C: , even if you have multiple visible primary partitions.
Meaning, when booting the Windows PBR, it will see its partition as C:, with the DOS/FAT16 primary partition (even if it appears before in the MBR) as D: .
DOS only sees its own FAT16 partition so it will always be C: anyway.
Only during Win setup itself you may need to hide the DOS partition.

I used to have this setup with Partition Magic's bootloader (iirc), but grub4dos is so much better (and scriptable).

gn0me wrote on 2022-03-22, 22:24:

Thread resurrection, apologies. I ran into this issue and when using DOS 7.x, some applications identify it as running Win9x and thus won’t complete the install process.

SETVER the installer and it should work...

Moved to Marvin -> Software.

gn0me wrote on 2022-03-22, 22:24:

Thread resurrection, apologies. I ran into this issue and when using DOS 7.x, some applications identify it as running Win9x and thus won’t complete the install process.

As mentioned above, creating multiple primary partitions and then installing a 3rd party boot loader into the MBR is probably the way to go.

It may be easier to hack those applications. Like with CTCM/CTCU.