It's a low power kit. I think you just have to help it with pedaling on hills. Here's my thoughts on about your two batteries. Any changes you make are at your own risk. Although it's only 24V, still a lot of power in the batteries, They can overheat and catch on fire if you do something wrong.
1) Two controllers can't run on the same motor. They're not designed for it and will blow each other up.
2) Connecting two batteries in series to make 48 volts will blow up the controller, unless it was designed to withstand 48 volts. Might take 36 volts though.
3) Connecting two batteries in parallel will increase range. Might increase power for hills, if the one battery can't supply enough current. I don't know if you could tell the difference though. There are concerns and cautions when you parallel batteries, but I won't cover them. Do your research.
You could ask Hilltopper if your present controller will work with their 36 volt battery. If not, you buy their 36V unit. Then their 36V battery would make the wiring easy. A sticking point is that they use a bigger motor in the 36V kit, so they might tell you not to do this. An alternate is a third party 36V controller/battery, but the wiring is much more complex, and controller wiring info is almost non-existent, and you still have to worry about the motor reliability. That's your call.
Looking at reviews on Amazon, they got users in San Francisco giving it 5 stars. Can't be that weak, or they're riding 350W kits. I also have a 250W Bafang motor on one of my bikes, rated for 36V. Can get up to 20 mph. No problem with local hills, as long as I pedal.
