My last job was a little similar, and only towards the end did I realize how other people dealt with this. Here is what they did (I never did it):
Get to work kind of early, put your stuff on your desk, fill coffee mug, etc. Make it look like you're there. Re direct your office phone to your cell.
Take your laptop or books you want to study to the nearby coffee shop, and do whatever you want there - side projects, learning, teaching yourself programming languages, etc. etc. Be sure to answer your cell and respond to work emails.
Come back into the office around lunch time and sit in the lunch room to eat, then head out again for the afternoon.
It's easy to cover your tracks by saying you were in a meeting, or working with so-and-so, or whatever.
It took me a long time to understand it was better to do the above, than it was to sit at your desk and be seen to not be working hard (i.e. reading a programming book, or reading HN)