does htaccess affect permalinks?

I tried to make my wordpress account work with multiblogs and I changed my htaccess file like it asked me too I’m now having problems I’m guessing with the permalinks cause every time I try to click a single post it directs me to 404.php template I looked on wordpress codex and entered the htaccess file from there but it didn’t work I was wondering what to do now that the links to my blogs aren’t working