From conversations with Diamondback on IRC yesterday here is my understanding of installing framework apks. First you need to Open Settings>apktool>frameworks. Then you need to decide on a tag for the framework set you are about to import (tags allow you to have multiple sets of frameworks installed for different ROMs at the same time) - I was working with frameworks from the PKMN ROM for One X so I settled on PKMN_OneX_1.0 for my tag. Add that in the 'tag' text field and then click on 'Add framework'. You then need to do this for each of your framework apks (I'm working on a Sense ROM so I needed to import framework-res, framework-htc-res, and com.htc.resources all under the same tag). Then once you've done that, still in the frameworks window you'll notice that there probably aren't any files showing in the list box. To get the freshly imported files to show up I then had to enter the filepath to the frameworks folder in the text box at the top of that window (so in my case C:\Documents and Settings\User\apktool\framework) and once entered in full the framework files now show up in the list.
Then when you create a new project, BEFORE you import the apk you need to right click on the project, select Properties, and then in the Import Tag dropdown select the tag you have just created. You can also change the apktool version/path just below that to try decompiling with different versions of apktool if you have any problems.
Hope that helped