WordPress MU

Does MU delete the existing .htaccess then try to recreate it or try to write to it? I have followed the directions given. I have changed the permissions to the .htaccess and then ftp'd in and deleted it, that didn't work, then I just changed the permissions of the .htaccess and that still didn't work, I have even tried simply writing the .htaccess myself but that to didn't work as it can't complete the install process, then again I tried installing to a subdirectory and then copying over to the root and then wanted to go into the wp-config and simply change the base url there but it wouldn't let me change the permissions to it or write to it at all even through cpanels file manager, so I completely open and am actually begging at this point for any help and information I can get to help.

Ok for reasons I don't immediately know, my second attempt to change the permissions of the .htaccess and then deleting it via ftp then running the install worked, the first attempt had not. The only thing I changed the second time was change the permissions of the .htaccess to 777 instead of 646. That shouldn't have made a difference but like I said, the second attempt did succeed.