It does not matter that your OS is 64 bit, since custombuild works both OK with 32 and 64 bit. Of course you should take care to make backups, and custombuild will do backups of all DBs if it's enabled in options.conf.
Regarding what might happen with your web-sites, I have no answer for you, as I know nothing about your sites. I doubt that upgrading of MySQL might break your sites... by itself. You'll need to recompile PHP as well, and there might be a downtime if your current PHP aren't able to load some MySQL lib files. As soon as PHP will be re-installed everything should work OK. Of course there always might be a chance to break anything. So if you want you can hire somebody to do the job for you. Feel free to PM if you need a private help for an amount of money.