The biggest safety danger with rechargable lithiums is during the charging process, it's best practice to charge in a well ventilated area (like out on the back porch or garage with an open window) and in some manner of non-flammable enclosure. Now there are millions of lithium ions in phones and computers being charged every day indoors, but that works because the device usually has built in charging and protection circuits to prevent cell damage and fires. Most lithium ion cell chargers like we use are kinda "iffy" on quality at the best of times, and not all cells have protection circuits.
The other one is running unprotected cells in series, and letting them drain down too far (or sometimes running two cells where one is damaged or defective) This causes a reverse charge and most of the nasty kabooms associated with lithium cells. There's a subforum here called "smoke , fire, and hot cells" that has lots of examples on what batteries do when they stop working properly. Protected cells in series are usually okay, if you run unprotected cells in series, or even a single unprotected cell for that matter it's a good idea to keep tabs on the voltage until you get a sense for when you need to charge them, as the cells can be damaged permanently and rendered unsafe if you drain them too far.
As far as general use, charge lithiums whenever you want, they have no memory, and very low self discharge. Keeping them charged to 100% all the time will shorten the overall cell lifetime, so I like to run cells down a bit closer to empty. Figure out how much you really use them and develop your own charging routine that works for you, and keeps the cells out of the red zone (under 3 volts). 2.5v is what most protection circuits will cut off at, but at 3v lithium ion is past the empty stage.