SciFinder, head and shoulders above anything else for checking references and synthetic methods.
In your lab book, there are a few things that you need to have for every single reaction, or it will be worthless for anybody following you.
1) Where did you get your procedure from? Note a reference for each procedure, so when you go back to write up your research, you will know where to give credit and footnotes.
2) Where did you get your starting materials? If commercial, that should be noted, but if they are products from previous reactions or were obtained from labmates, make sure that you can trace them back through your notebooks! I label all my compounds in the format ([lab notebook name]-[page number]-[product on page]) so they can always be traced back. For example, a crude product for a reaction might be MLC25-136-1, and after a chromatography that isolated three spots, I would have products MLC25-136-2, MLC25-136-3, and MLC25-136-4. That becomse the name of the compound whenever I use it again, so I can always trace back every batch of compound to its source from commercial materials.
3) How did you identify your products? It helps to have a standard set of analytical data for every compound, but at the very least you should have whatever data you based your identification of the compound on. If you compared it to literature values, be sure to include the reference for those values as well.
The rest of the lab notebook record is all that stuff they taught you when you were taking organic chemistry - the reaction you were trying to carry out, a table of the amounts of each compound you used to carry out the reaction, a brief description of how the reaction was run and how each product was isolated, purified, and characterized, and the identification and yield of the product(s).
Organizing the workbench - that is about as individual as it can possibly be. Take care to follow the OSHA guidelines if you are working in the US, and keep an eye out for Murphy's law. Pay attention when you are working to times when you almost break or almost drop something, and try to move things to avoid those problems.
And some beginner safety tips, although you didn't ask this one. When you start, make a practice of understanding the possible risks and remedies for every compound you are using. Know where to find the eyewash fountain, safety shower, and fire extinguisher. Keep everything clean - if you spill something, clean it up immediately, and be aware of places that other people might have spilled things. Bad accidents aren't usually caused by a single mistake, but by a whole series of little things neglected. Resting a hand on a bench, you accidentally press onto a glass sliver that wasn't cleaned up when somebody broke a beaker last week, and when you jerk your hand back you spill a flask of strong acid that shouldn't have been there into a sink full of water, which sprays up into your eyes because you had just taken off your safety glasses, and now that you can't see, you can't remember where the eyewash fountain is and when you make it to the safety shower you can't figure out how to turn it on...
Best of luck - you're entering a fun world!