When using a device with that much power in front of your face any precaution taken is prudent.
Never pair batteries of different chemistry. Never pair batteries with different ratings. Always pair new batteries of the same model. Always use IMR or Hybrid high drain batteries rated for your device.
Of all the advice so far, this is the most crucial. NEVER pair batteries from different vendors, or with different chemistries! When marrying two batteries, buy them both at the same time, from the same vendor, and ALWAYS use them together; don't borrow one for your mech mod!
When batteries are used in series, the stronger one will bully the weak one.
When batteries are used in parallel, a weak one can "slack off" and make the stronger one do most of the work. So if you have 2 "20A" batteries, and expect to get anywhere near 40A from them, they better be very well matched; otherwise you might be drawing 35A from the strong one, and only 5A from the wimp. This is particularly important if you need the 2 batts to get the current you're looking for.
When used in series, the reason you rotate them is that the top one gets some heat from the coils; this lessens it's capacity (both on a single charge, and over time). Both batteries are supplying identical power, but the heating effect does make a measurable difference. BigCatDaddy is almost, but not quite correct; in series, both batteries are providing exactly the same "juice", but the heating lowers the battery efficiency.