These are just a couple of suggestions that I have for when you are going to upload a journal article (since I just fought through the Optics Express™ awfulness). So, without further ado, here it is:
This list is in no particular order, in spite of the numbering system
Set aside several hours in advance for this
Look ahead at what you're going to need (just go to the submit system and look over what they say you need)
Build a list of people that you can use as reviewers (these need to be people that you don't work with/haven't worked with for 5 years)
Smalley can likely help out, but if you're looking at Graduate Schools, a professor with a close subject matter may a good choice, too
Keep snacks handy (and if you feel the need to curse, maybe make sure no one else is in the room)
Have all the information for anyone that may need to be added (e-mail, name, address)
Address for fellow students (such as co-authors), can just be listed here at BYU (I use this room and you can too!)
ALWAYS check their version of the PDF
At the end, make sure to look at what their PDF creator did to your paper
If you are near your page limit, this is important
If you use figures in your paper, this is important
If there are titles in your paper, this is important
Adjust the paper to make it look right as a PDF
If you're uploading extra media (like a video), have descriptions, etc prepared beforehand
If you're unsure about something, contact someone who knows (probably Smalley)