Uploading files

I am uploading my files via your file manager as I can not connect using FTP, I always get this error “530 Login authentication failed”. I have 3 folders, css, js & images, I can upload my css files to my css folder but when I upload my js files to the js folder it then removes the css files from its folder. How am I supposed to upload all of my files

Never mind, I was trying to upload in the root and not the htdocs folder