If the NTFS partition is being read by ManaGunZ then it's properly partitioned. The problem seems to be the FAT32 partition which the litmus test being whether or not it is detected on the XMB. I'm not sure what you could do, but maybe someone else will be able to advise on if/how you could redeem PS3 access to the FAT32 partition without having to format the entire drive.
I have a 2TB external HDD with both a FAT32 and NTFS partition, and have no problems whatsoever. I too store my PS2 ISOs on the NTFS drive when I want to free up some space on the (stock 160GB) internal drive. So, it is very possible to get the PS3 to read both FAT32 and NTFS on the same drive.
Again, I'd hold off until someone else can offer their opinion, as I'm not sure what the best solution would be and I hesitate to suggest formatting the drive as that may be totally unnecessary.
Sorry I couldn't be of more help, but I'm just not too sure myself on what's best to do in this scenario.