I have tried a lot of PDF Readers apps for my iPhone. But the best one so far has been PDF Reader Lite by Kdan Mobile Software LTD. There are many PDF Readers like iPDF, PDF Extreme, Reader Lite, and many more in the iTunes store but it seems most of them all have tried to renovate PDF Reader Lite and failed. It's a powerful file viewer too, which supports different formats like .doc, .txt, .ppt, .jpeg. It is very easy to use and powerful tool for your device but the Lite version only allows to store files no more than 10 files. If you like the Lite version you can consider to download the full version via iTunes Store.
For uploading the files to your apple device you simply can connect your device and your computer via WiFi and send files by using FTP or your web browser. The other way to upload files to your device is by using an application called iFunbox. It is a tool to transfer, manage, browse and explore your files, epub documents, mp4 videos and mp3 musics for iPhone, iPad and iPod.