Ok, so, My problem is that if I right click I go into strafe mode. I have eDuke and when I try to set Strafe to a button, hitting A or D won't do anything.

I 've read other posts and people say to go to SETUP but I get the problem of it saying I need a 32 or 64 bit which I have 64 bit. I don't get it when people say the start menu. Please help.

Run Duke Nukem 3D from the eDuke32 launcher, then select Options-->Keyboard Setup. The bindings for Strafe Left and Strafe Right are below the "Look (Direction)" keys. Just "Strafe," IIRC, is a modifier key that toggles turning (with the keyboard) into strafing while it's held.