I'm planning on installing 3. I'm presuming it will try to integrate my old projects, but which library will it try to do this from are there any potential conflicts I need to be aware of? For example any other files located elsewhere involved.
Aperture 3 will try to launch any library called 'Aperture Library' located in the '~/Pictures' folder by default and certainly on first launch. If it starts to load the Aperture 2 library named 'Aperture Library' you should see a dialog telling you that the library will need to be updated before Aperture 3 can work with it.
Personally, I would rename the Aperture 2 libraries to anything other than 'Aperture Library' and move them out of '~/Pictures' folder if any currently reside there.
There are Application Support / Aperture folders in both the '~/Library' and '/Library' folder for sure, and there may well be a 'com.apple.Aperture' folder in '~/Library/Caches' folder that may create issues - although I am not sure on that point. When some users upgraded from AP2 to AP3 during original release, many resorted to removing and/or deleting all Aperture related contents from those folders to fix performance, crashing and failed library upgrade issues.
You might create a folder on the desktop to hold the contents of the Application Supoort / Aperture folders for the AP 2 stuff since this will have plug-ins, import and export presets, etc. you are using in AP2.
Note - there is also a 'ProApps' folder in '/Library' that had always held a system ID file used for licensing Aperture 2, but I am not sure if that is of any consequence.
You may already be familiar with the Aperture 2 troubleshooting basics information, but here is the link which among other things mentions support file locations:
http://support.apple.com/kb/HT2945
Lastly.. is it possible (and more stable) to keep Aperture 2 separate and only go in there when I need to? Is this recommended and would it create any conflicts?
You should be able to rename the current Aperture.app to say Aperture 2.app in the applications folder. This should allow you to have both AP2 and AP3 co-exist on your system without issue. This was Apple's recommendation for the Aperture 3 trial when it used to be offered.
Note - you would launch an Aperture 2 library with Aperture 2.app by dragging the library icon onto the app icon since Aperture 3 will become the default app OS X will try to launch if you double-click any of the libraries.
If it were me, I would rename the Aperture 2 libraries and not use Aperture 3 to upgrade them (at least for now) as well as renaming the Aperture 2 app as described above to allow use of both as needed.
At the bottom of the linked release notes below are some hints on upgrading libraries from Aperture 2 to Aperture 3 if you decide to do that instead:
http://support.apple.com/kb/TS2518
As always, make sure you have good backups before proceeding.