well its pretty much in the link i posted a few posts ago about installing java/limewire.
chmod is just changing the file to an executable followed by numbers which tell it who can run it i believe.
chmod 777 is what i always use because that makes it executable for anyone to run i believe. usually apps like .bin files need to be changed to executables in order for you to install them.
about the .bash_profile. this usually pertains to drake/redhat/suse(maybe suse, not too sure) limewire will crap out if it doesnt find java on your machine so you need to put the path to java in your profile. you can verify this by typing "java -version" in a console.