Uploading a contract just to staple two PDFs together is an odd trade. The merge tool in SKY13.app reads the files in the browser tab and writes one PDF you download. Close the tab when you are done and the working copy goes with it.
Add the files in the order you want them read. If a scan arrived last and should be first, remove it from the list and add it again at the right moment, or merge first and then use Organize to move individual pages. Each file needs to be 80 MB or smaller.
A password-protected PDF will not merge here. That is deliberate. Open it in the software that knows the password, save an unprotected copy you are allowed to share, and merge that copy. Do not use a random website that asks you to upload the locked file and the password together.
On a phone, give the tab a quiet minute. Mobile browsers can do the same work as a laptop, but a large stack of scans uses memory. If the phone warns you, split the job into two merges and then merge the results.