Should I connect it to Channel 1,2 line input or Channel 3,4 line input?
Channel 1,2 line input: Standard 1/4” (6.25mm) Jack socket for balanced or unbalanced line level signals. Wired Tip=Hot(+), Ring=cold (-), Sleeve=Chassis
Channel 3,4 line inputs have a high impedance jack input capable of taking either a normal line level or a low level input from a guitar pickup.
The only difference between mono inputs 1-2 and 3-4 is the Hi Z inputs for guitars or other instruments.
As far as I can see from your description (and briefly checking that website you linked), I would use Channel 1,2. By the way, it won’t harm anything if you decide to use other channels. You could try both, and select the one that sounds the most pleasing to your ear.
I am not completely sure whether BeatBuddy contains input signal buffer or not, but as the sound will not go through if BeatBuddy is powered off, some electronic circuitry is definitely used, so most likely the signal is normalized. BeatBuddy can adjust volume level of the input signal, but no further processing is done.
When you said acoustic guitar, did you probably mean electro-acoustic? Unless your guitar have a pickup installed, you won’t be able to plug it in.