There's no serious danger in using Disk Manager or any other drive geometry "shim" utility, as long as you take the proper steps when repartitioning or moving your drives.
The main problem occurs when you install a drive as a slave in a two-drive system, partition it with Disk Manager (which installs the hidden Disk Manager software on the master drive), and then swap the two drives. When you attempt to boot the computer with the new drive, you'll receive an error message saying that the partitioned drive is unreadable: The Disk Manager software is no longer on the boot drive and hence isn't loaded.
Disk Manager won't affect performance, and as long as you have Version 7.03 or later, it should work without a hitch with Windows 95. My only gripe with utilities like Disk Manager is that they insert an extra layer of complexity into configuring your hardware. New hard disks and controllers remove much of this complexity: Just plug them in, and with a few exceptions, the rest is automatic.
If you're planning on upgrading your system board, BIOS, or disk controller -- any of which will likely allow you to transcend the1024-cylinder/512MB hard disk ceiling -- you should remove Disk Manager. That's simple enough: Back up your hard disk, partition and format it with the fdisk and format commands, and then restore your backup.
- Scott Spanbauer