Generally, you secure each PDF with its own password (if you wish you can use the same password but from Acrobat's point of view they are not related). When you add content PDF retains the password with which it was originally secured. PDF has two passwords: one for opening PDF and one for changing permissions. The second password also opens PDF. If you secured PDF with permissions password then you can change passwords on a PDF any time you want.
Your question, I think, is a slightly different one. You want to save several Excel documents as secured PDFs. If you do that for each Excel document separately, then you choose password each time and it can be a different or the same one as you wish.