Thinking of the iPad as a thumb drive is going to cause you problems down the road. It's easy enough to get PDF's onto the iPad and read them there, but if you are expecting to easily copy them back to a computer it will be less convenient; though it's not impossible.
If all you want is to transfer PDF files to the iPad so you can read them, with some basic highlighting and notes, then iBooks will work fine. For one or two PDF's at a time, you can email them to yourself, then use the Open In iBooks feature in Mail on the iPad. Or you can use the File Sharing feature of iTunes and a USB cable.
In mail, you either tap on the file icon, or in the center of the PDF (if it is shown in-line) to get the Open In options. This makes a copy of the PDF in iBooks, then opens it in iBooks.
To use iTunes on a PC, you add the PDF to the iTunes the computer, then use the sync settings to enable book syncing, and sync the iPad. I don't recommend this for just adding books to the iPad. Here is Apple's Support page on syncing. It's mostly about music, but the general method applies to books as well.
iTunes 12 for Windows: Sync iPod, iPhone, or iPad
If you want more extensive abilities the three main PDF apps I have and like are GoodReader, PDF Expert, and Documents 5.
GoodReader is PDF reader/annotation app with good tools, a flexible file system that will store almost any file format (but only display a few). It's not the best interface, but will do file management tricks most other apps can't handle.
PDF Expert by Readdle has some of the best PDF annotation tools, and it will let you edit PDF files at a page level (delete pages, add blank pages, paste in pages, split and merge files). But it only works with PDF files.
Documents 5, also by Readdle trades of the more powerful PDF tools for a wider range of file compatibility. Most document and media types can be stored and viewed (played) in Documents. Some of the simpler ones can be edited and/or annotated. If you get both PDF Expert and Documents, you get all the power of both.
All three if these have multiple ways to transfer files to/from your computer. All the usual Cloud file services are supported (DropBox, Box, Google Drive, OneDrive), and if you know what you are doing you can also use FTP, SfTP, WebDAV, and even Windows SMB protocols.
In addition they have what they call Wi-Fi Drive (or Wi-Fi Transfer in GoodReader's case). When turned on in the app, you are provided with a URL (web site address) that is generated by the iPad. This is a local site, not visible outside your own wi-fi network. To transfer files you go to a computer on the same network, enter the URL in a browser, and use the tools on the provided page to copy files back and forth.
GoodReader used to have a companion app for the computer called GoodReader USB. It may still exist (I haven't looked recently). This app can be used on the computer to copy files back and forth using a USB cable.
How I use these app;
iBooks. I use this for PDF files that I intend to keep permanently, have not specific purpose (so they don't need extensive organization), and that I only need to reference or read. I also use it for what it's intended, to read iBooks and other ePub formatted books.
PDF Expert is my main PDF app. I use it when I know I want to annotate a PDF, keep PDF files organized in folders for specific projects or categories, and/or want to keep those PDF files synced with a cloud file service like DropBox.
Documents 5 is an app I picked up out of curiosity. If I needed to keep a lot of different file formats organized in one place, I would use it: for instance, some pictures, audio files, PDFs, and some Word documents all about the same project. But I never do this. I prefer to keep each file type in apps, which are best suited for what I want to do with those files. I can get away with this because I don't have a lot of complicated projects with lots of related files of different types.
Note: PDF Converter by Readdle is handy for converting other file types (even email content) into PDF files; and it integrates well with PDF Expert. It won't do everything, but nothing will.
