I recently installed PM version 2 and I left out the web portion. Can I go back and install just the web portion? Would this be recommended or should I put it on its own web server?
You can indeed go back and run the installer to just install the web portion. Although I always recommend to run Orion on a separate server, you can get away with co-locating these products. It just comes down to available resources on that box. Here's what it should look like when you re-run the installer.
