Similar problem
I have tried many things. I had a sub directory with the entire store in side and was able to get to the powerstore3 index file by adding the directory to the address which kick started the store creation.
i.e. testserver/site name/ecart <--I added ecart once I opened my site homepage.
this let me generate the store but as soon as I logged into the admin there was a parse error that made it unusable. Error below.
Parse error: parse error in C:\wamp\www\oaksteadmed\WA_Globals\WA_Globals.php(58) : eval()'d code on line 1
So then, I renamed the powerstore index file to ecart.php and moved the entire store into the main site directory. Made a link in my navigation link to the ecart.php and was able to recreate the store. but got the same issue as above.
Then I created a test store with nothing else and everything works fine just as described by WebAssist. There must be a way to integrate this powerstore3 into another site but I haven't had any luck and can't seem to get an answer on how. I would think this is common practice and a tutorial on how to would be nice.
Maybe someone can help us both.....