I filed my taxes online and sent it in. Then got another w-2 in and had to send in the mail an amend, will i get two different checks, online and through mail?

Yes, if you filed the original return online and asked for a direct deposit of your refund, then that will take place no matter what is on your amended return.

And if you are due an additional refund because of the amended return, then that additional refund will be mailed to you as a check.