As far as books, I highly recommend The Complete Book of Woodworking: http://www.amazon.com/The-Complete-Book-Woodworking-Detailed/dp/1890621366/ref=sr_1_1?ie=UTF8&qid=1335885982&sr=8-1. It's easy to follow even for the uninitiated. It goes over the major tools, what they are used for, and has excellent instructions on some starter and intermediate projects. There are even some workbench projects toward the end, one of which is made only from plywood and 2x4 lumber. I made it with a jigsaw and really uneven cuts, and it's held together well for about a year (it's usable for everything except hand planing). I'm also a software engineer by trade and learn well from books, so I spent a good few months obsessing over this book in my apartment before buying a house and really getting started.
For video instruction, The Wood Whisperer is one of my favorites; he gets into what tools are used for, how to set them up and tune them, and has some videos dedicated to safety. He's also very technical and comes from a science background, so the engineer in me relates well with him. He doesn't leave out many details. Fine Woodworking is also very good and for $5 a month you can get access to a ton of video content.
http://www.thewoodwhisperer.com
http://www.finewoodworking.com
SawmillCreek and WoodworkingTalk are nice forums to search through for tips and discussions about what tools are best used for what projects.
http://www.sawmillcreek.org
http://www.woodworkingtalk.com
Most of these will discuss fine woodworking, furniture making, and detailed joinery, which you may or may not be interested in. All of them, however, will give you information you want about tool usage. It may be more detail than what you're interested in for the projects you describe, but if anything you'll be over-prepared.
Best Answer
The trick here is to actually have the lid start out as part of the box, so that the grain of the wood all runs right across the separation between box and lid.
One way this can be accomplished is to build a solid "block", and then turn that into a box. You first cut off a "lid" off of the solid block, and then by one means or another, hollow out the inside of the box part.
Then you would often use a belt sander or just sand paper on a flat surface and tidy up the two mating pieces (lid and box lip) so that imperfections from the sawing go away and leave an imperceptible gap between the lid and the box.
Since the lid "came from" the box originally, it will all match up and look like a single piece of wood if you get your gap perfect enough.
To better understand the techniques, search on YouTube for "bandsaw box". It is a "thing" in the woodworking community. Some people specialize in making small boxes similar to what you've described but for decorative rather than deceptive use.