The only issue with parallel LiPo batteries is that large equalization currents can occur upon connection if there's a big mismatch in state of charge. LiPos are typically very high drain so it's not a problem for output, but there's a factor of around ten between output current tolerance and input current tolerance. So if they differ enough in state of charge it's possible to exceed input current tolerance on one of the batteries.
Once batteries are connected in parallel and equalized, they behave as a single larger battery. For safety considerations your option is to either permanently connect them or simply use a single larger battery with equivalent capacity.
You need to protect LiPos (or any Li-Ion battery for that matter) from over-discharge and over-current. Typically off-the-shelf ESCs have over discharge protection where minimal voltage levels can be programmed through software. Some even have over-current protection, though it's not typical.
It's a bit involved adding over-current protection with high current devices. It's done with a current sensing circuit and an input power MOSFET that shuts down the circuit when excessive input current is detected. That's not a particularly difficult circuit to design, but it does call for a ucontroller. A low pin count 8 bit device can do the job with a few lines of code.
For lower currents Li-Ion protection boards off the shelf can do the job, but you don't find them commonly with high enough ratings for electric motors doing larger mounts of work.