I'm assuming you filled out the application online and then sent the documents in after they e-mailed you asking to do so?
For me that email said step
***
.
Then the next email came after they received my documents and issued my visa and it stated step
***
and it included a link in the e-mail to go back into your original application, change your answer to the question if you have a visa from no, to yes, then upload that visa to your applcation.
Uploading the visa after you receive it is step 3, and then you just wait for the COE.