my WP blog is in a folder, not in the root.
Now, by default W3 total Cache is using my root .htaccess for some reason, as opposed to WP Super Cache, which modifies the .htaccess in the folder.
This gives me two concerns :
1 - The added rules slow down my other blog which is in another folder.
2 - I fear that I may get conflicts if I try to use W3 Total Cache on my two blogs.