Thanks for getting in touch! I'd be happy to help out with this.
You can load your list of targets in PingPlotter via the "File" -> "Load Target List" option in the program. You'll want to make sure your list is properly formatted so PingPlotter can read it, though. A .txt file where your targets are listed out one per line should do the trick. We cover this in a bit more detail here (under the "Loading a List of Targets" section):http://www.pingplotter.com/manual/tracing_to_multiple_targets.html
Once you've got your targets loaded up, they'll automatically be added to a workspace in PingPlotter Pro. If you're interested, we go over workspaces here:http://www.pingplotter.com/manual/workspaces.html
At this point, PingPlotter *should* automatically load up your workspace (with all of your targets) after each server reboot. If you should find that it's not, you may need to make some adjustments to your auto-save settings in PingPlotter to make sure your targets stick around like you'd expect them to. We've got some documentation, as well as a short video that cover PingPlotter's auto-save settings here:http://www.pingplotter.com/manual/auto-saving-data.html
Please let us know where this leaves you, and we'll be happy to help out from there!