Are you doing standard ILR or the likes of Super Priority ILR?
When I did the Super Priority ILR for my wife, there was no app, and while we scanned and uploaded all docs onto the website, we were never asked for physical copies. That may be different for standard ILR. Ksand24 and larrabee will probably know best.
Here's what I wrote here for our ILR earlier this year.
Use mbmoffat's thread at
https://talk.uk-yankee.com/index.php?topic=100139.0 for reference.
1. Collect all your documents as per the thread mentioned. There's a few iterations on what is needed but page 8 has latest view
2. Apply at
https://www.gov.uk/government/publications/application-to-settle-in-the-uk-form-setm/apply-online-form-setm3. At 2 you can save and carry on to next section until you have all the data ready to go. And go back to start to recheck data
4. Once you're happy with all the data, plus you have all the documentation and scanned into pdf (actually PDFs need uploading 2 days before Biometrics so you have time to prepare after this bit) then there is a choice before you Submit
5. Standard is £2404 and Super priority is £3204 BUT Super Priority option only appears at 1am BST !! -->>> NOW MIDNIGHT DURING GMT
5a. So wait and do not Submit until you get the option of super priority. If it doesn't appear try next day. I saw it first time I tried.
6. Refresh before midnight and you just see standard. At midnight you see Super Priority pop up. Select it and Submit the application.
7. You pay the money and then get a code emailed to applicant to log into UKVCAS website (run by Sopra Steria)
8. Follow the link in email to UKVCAS website to register and then enter your postcode and find where Biometrics are available.
9. I think (experts will confirm) that only so many are release each night. So pick quickly, but dont rush it
10. Be sure to give yourself at least 3-4 days before Biometrics as you will want to upload your pdfs 2 days before Biometrics. And it's nicer to recheck the pdfs.
10a. Only when at UKVCAS after you upload all your PDFs and then Submit are you ready for Biometrics
11. Biometrics. Take your passport/BRP and the big QR print-out that is emailed to you after Biometrics location/date is chosen. I brought along support documentation but it was never asked for.
12. ILR approval the next business day.