Actually, they need to be in the same state of charge before CONNECTING them in parallel. If you connect a charged cell to a discharged one, fireworks may ensue. Once connected in parallel, it is impossible for them to be in different states of charge.
Lithium ion batteries are actually pretty easy to charge properly. You have to do one thing really well, one thing reasonably well, and one thing okay.
What you have to do really well is the voltage. At 4.1V a cell will take pretty nearly a full charge (IIRC it's around 95%). At 4.2V it will take a full charge, but will take fewer charges before it starts degrading. At a little over 4.2V, it starts degrading much faster.
What you have to do reasonably well is limit the current. To do this you have to know your cells and your goals. Many cells are ideally charged at 0.2 to 0.5C. Some can handle 1C or even much more without a significantly shortened life. You have to know what your cells can handle, and choose how fast you want to charge vs. how many charge cycles they need to last.
What you have to do okay (actually you don't even really NEED to do it at all) is terminate the charge. Once you have your voltage and current limits set up, you hook up the battery and it starts to charge at the current limit. The voltage begins to rise. Once the voltage hits the limit, the battery starts to take less and less current. Once the current drops to 0.05 - 0.1C, you should stop charging. Continuing to charge beyond this point is called a 'float' charge, and will simply result in a shorter battery life (this is not true of all chemistries - Lead-acid batteries love float charge). The lower your voltage limit is, the less critical charge termination is. For best shelf life, a LiIon cell should be kept at around half-charge, or about 3.7V. So a float charge at 3.7V would give great shelf life, but would only keep your batteries half charged. Anything above that is a trade-off.
Cheap hobby chargers can actually do a pretty good job of charging your batteries, especially if you charge and use them frequently. But once you know what goes into making the decisions, you can make a more informed choice about a charger for your particular application.