After figuring out that the programmers manual was outdated, I had to fool around with things to get this working for myself. Just thought I'd post how I did it so others could give it a try.
Note: You don't need to do this if the server is local, just turning on Just-In-Time debugging will work if you add the line 'System.Diagnostics.Debugger.Break();' into the code. Otherwise attach to the process 'w3wp.exe'. Also I'm pretty bad at explaining things for the most part, so feel free to point things out.
Also, the process 'w3wp.exe' will only run once you have Innovator open and are trying to run code, as far as I've found at least.
First set up Remote Debugger on the server computer. Make sure to uncheck the 'run as a service' option.
http://msdn.microsoft.com/en-us/library/bt727f1t.aspx
Now run Visual Studio 2010 Remote Debugger, go to Tools -> Options and set it to No Authentication and choose a port, then set it back to Windows Authentication. (for some reason we couldn't get it to connect with No Authentication O_o)
Then set up the firewall, using the port you selected above instead of the one it tells you to use.
http://msdn.microsoft.com/en-us/library/ee126350.aspx
Once that's done open up your Control Panel, go to Administrative Tools then run Computer Management. In here open up Local Users and Groups and click on Users. Go to Action -> New User and add an account that has exactly the same username and password as the one you use to log into the computer you're trying to debug remotely from. Once that's done make sure the user is in the Administrator group and close that window.
Now open up Internet Information Services from the Administrative Tools window and press the arrow next to your computer name on the right. Choose the first option under your computer name, right click on Aras Innovator AppPool ASP.NET 2.0, go to advanced settings. Scroll down to Ping Enabled and switch it to false, and set Ping Maximum Response Time to 300 or greater.
Lastly open up 'C:\Program Files\Aras\Innovator\Innovator\' and share either the 'Server' folder or the 'Server\dll' folder so that the remote computer can find the source file to look at.
Log into your Innovator server (hopefully a test environment!) and run Visual Studio 2010 on the remote computer, then go to Tools -> Attach to Process and in the Qualifier box put the the server name that Visual Studio 2010 Remote Debugger shows to connect to. Select 'w3wp.exe' and hit attach. Now if there's an error or you have the line 'System.Diagnostics.Debugger.Break();' in your server side code it should automatically open up in VS2010.
Wall of Text crits readers for 20k! Anyway, tell me if that works for anyone else, or if it's too confusing to understand. That's what we had to do to get it to work. Enjoy.