First, for higher performance and reliability, I would make part of that new drive my C: drive. That would require moving the primary partition from the old drive to the new one with a program such as Partition Magic, Ghost, etc. (FMI, see http://duxcw.com/faq/hd/hd.htm) or doing a clean install on the new drive, copying your user data to it, and reinstalling all applications (that is what I would normally do on my computer).
Now to answer your question… As far as know the hard disk drive partitions will occupy the first few drive letters, followed by the CD-ROM drive. I presume that you are having problems accessing your CD-ROM from applications/games that were installed when your CD-ROM drive had the other drive letter. Some applications games can be reconfigured for the new drive letter, others have to be reinstalled—another reason for a clean install.
There is a way, however, to separate your hard disk drives from one another so that the partitions are not intermingled. Only the first drive/partition should be partition as THE Primary DOS partition (and then made active). If you partition the rest of the drives/partitions as extended partitions, the logical drive letters assigned to them will be grouped by physical drives. That is, Primary DOS partitions are assigned drive letters first, followed by extended partitions. The Primary DOS partition has to be created first. The hard disk with the Primary DOS partition has to be connected to the computer in order to partition other drives/partitions with extended partitions. This then becomes dangerous procedure as far as any data on an existing drive (Primary DOS and extended partitions) is concerned because of the possibility of human error in selecting the correct drive upon which to create a partition and to format. I strongly recommend a backup any critical data, My Documents, C:\windows\favorites, C:\windows\cookies, C:\windows\*.pwl (password file), mail box, etc. before attempting it and be especially careful to be sure which drive/partition you are operating on. To my chagrin, I have made this error few times, usually when hurried or when doing other things in parallel. I would make that C: drive about 4 GBytes. Anything larger will take too much time to defrag. Larry