You should always install oldest OS first . Also note the booting for these two OS's if want to use dual boot and windows boot manager will be done from the first drive despite installing OS on 2 different drives.
As commented this is defined in the Boot.ini file on the first drive. Most windows and DOS versions have strict limitations on where boot initiates from.
If you want the two to be completely independent you will need a third party boot manager that will usually create it's own mini partition that it then controls boot locations from. The advantage of this is that if you cahnge one drive you will be able to enable or rediscover the other drives OS.