An iPad is great for reading PDFs. Use a Table of Contents (TOC) to navigate a PDF easily inside your favorite PDF reading app. The slides below show how to locate the TOC in iBooks and GoodReader apps for the iPad.
PDFOutliner makes it easy to embed a TOC in your PDFs.
The PDF shown is Final Cut Pro X Unleashed, an excellent PDF ebook published by Digital Heaven.
You can read a long PDF faster by splitting it into shorter PDFs, and tackling one chapter at a time.
iAnnotate on the iPad is an excellent app for annotating and marking up PDF files. A companion app, Aji PDF Service for Mac, provides an elegant way to serve PDF files from your Mac to iAnnotate on iPad over a wifi network.
Use PDFExplode to split a long PDF into several short PDFs, say one PDF for each chapter. Then, markup one chapter at a time in iAnnotate and sync back with Aji PDF Service on the Mac.