This probably isn't hard to do but I ended up using diskpart in windows 2003 to align them to 1024 and formated them fat32 with 2003 I used assd tool to verify they were both aligned. I used BTTR BOOTMGR because of all the boot managers I tried its the only one that never complained about CHS and LBA ligning up or out right refusing to cooperate like PQ Boot from pq magic. It's also so small it fits in the bootsector and can hide partitions on the fly. Using somthing like Linux or any newer version of windows also borked my partitions and made them unreadible.

I needed to used 2003 or XP to format becasue they support Fat32X and multiple primary fat32x partitions. Other tools just use normal fat32 which doesn't always work on old computers. FAT32X enables partitions to exist beyond 1024 cylinders.

I wanted to do this becasue I don't have access to ISA in this one computer and have a Yamaha XG in it. If youre familiar with it you know that the drivers are kinda bad but when your game doesn't matter it works great well. I wanted 2 sperate windows installs on with VXD drivers and one with WDM drivers. Each set of driver offers its own quikyness and 1 will work with some games and not work with others.

For example DUKE3d work fine with WDM drivers if you used default settings in 9x native dos box but will crash windows if you use VXDs. Doom on the other hand will work good with VXDs in 9x native dosbox and glitch out with WDMs. The Dos drivers can work in real dos mode on either partitions so this way I get maximum compatibility a XG can give.

I Probably could of not bothered with aligning the partitions but you just get way more performance with them aligned.