How to design a Lithium-Ion battery pack?
Lots of questions!  Instead of just pointing you to a certain IC or battery, I will try to answer your questions so that you can understand the concepts and pick or build your own battery.


What precautions do I need to take so that there are no explosions?  Certainly something that is possible with lithium ion batteries!

A) Do not overheat.  You can find charging systems with thermistors that monitor the temperature of your battery.

B) Do not over discharge.  Lithium ion should not be discharged below 3 volts, but 3.3 volts is a better goal to aim for.  You Over discharging is more likely  to cause the battery to lose capacity than explode, but best to keep over 3 volts regardless.

C) Do not over charge.  Very important not to charge over 4.2 volts.

D) Do not short circuit.  Allowing the positive of the battery to come in contact with the negative for longer than a few milliseconds will likely cause a fire.  Usually the short circuits are accidental and there are circuits that will protect the battery if short circuit occurs

E) Do not discharge the battery at a rate faster than the battery is rated for.  Again there exist protection cicuirts that will protect against this.

F) Cells in series must be balanced.  Simply applying a current to the battery pack might result in some of the cells charging at slightly different rates leading to imbalance.  As a result it is a very good idea to monitor each cell as it is being charged. There exist IC that will do this. 
How does the use of boost and buck converters affect battery life?  Boost and buck converters are quite useful, but you will lose some battery life due inefficiencies.  Most of the boost and buck converters that I have seen have about an 85% efficiency although occasionally I have seen 95% efficiency claimed. Thus you lose 5-15% battery life due to inefficient conversion.


Don't forget that a fully charged 3 cell lithium ion battery is 12.6 volts - is this too high?

Good luck.