What is the specific error you are getting on your store pages when you try to add in the CMS content? If you have them both working successfully in their own directories then you should not have any problems using the CMS content on your Power Store pages. I think based on the structure you have described here that the problem may just be a linking issue to the include files. On your Power Store pages that you are putting the CMS content on you may need to put a ../ in front of the paths.