To "send in" something means to submit it by mail or email. It's similar to the word "submit", but "submit" can also be used to describe giving something to a person by hand, whereas "send in" cannot.
You "send in" a résumé, an application, a payment, or some other official document. You submit it to someone who has authority.
This phrase can be ordered two ways: "send ___ in" or "send in ___":
Have you sent in your application yet?
I sent my rent check in last week.
But always put "it" and "that" before "in":
I can't remember if I sent it in.