Sent from my BlackBerry 10 smartphone on the Rogers network.
Running a 3S LiPo/LiIo in a pack you need a BMS to balance and protect the cells from over/undervoltage. These are widely available on ebay, search for "18650 3s bms" or similar. For charging you need a CCCV power source, and they're also abundant on ebay, search "ac charger 3s 18650", make sure they have constant current mode and not just foldback limiting. These chargers will also work when powering the unit, but the charge complete led will probably not work until you shut it down.
Make sure to match the correct end voltage, LiIo 18650 is usually 4.1V and LiPo pouch cells can handle 4.2V.
Of course you can run them without all this, but YMMV. One mistake and they're either scrap or on fire. The Li+ are very powerful and packs a lot of energy compared to lead acid cells, so very pleasant to have in portable stuff.
Good luck with the build