Most of the time, I use PDF Arranger, since 90% of my work is either appending pages, or reordering one or two of them. Pages to be appended can be made using some document editor and exported as another PDF or image. I use rnote if I want to write handwritten notes over a PDF, or Scribus for modifying PDF texts, resizing, adding or removing them. Seems to work for most of my use cases. All the applications noted are FOSS.
In case none of those work, I either request the source for a more workable document, or just give up. Do note that none of them support signing PDF documents (or more likely: I don't know how to).