It's actually not a good idea to run Li-Ion batts in parallel. You can get over-current condtions if one is low and the other is not (one charges the other without bound). It's possible to run Li-Ion batteries in parallel safely with properly engineered cell monitoring and protection circuitry, but for casual modding, it's best to avoid it. If you want to run batteries in parrallel, it's much safer to use NiMH bats that don't have the volotility of Li-Ion batts.
Otherwise, mods with two Li-Ion cells are typically running them in series for higher voltage, either regulated or unregulated. Even then, it increases the risk of battery issue since there's the possiblity of high currents occuring in a battery that's discharged. When using series batteries, always match the cells and take them off the charger and put them in the mod in pairs. There should be a way to quickly and easily disconnect the batteries (such as master switch or quick release) if there is a problem of some kind. Never put Li-Ion batteries in a sealed enclosure.
Battery size and shape is generally a matter of preference revolving around form factor and battery capacity. It can also be a matter of safety. For example, running two LiFePO cells in series is much safer than running two LiCo cells in series. The safest configuration is a single battery. There are off-the-shelf boost modules you can use to run higher voltgage which is preferable to using multiple Li-Ion batteries.