On the Amazon link you posted, there was a diagram on how to install all the parts and pieces. You can connect the panels in series if shading is not an issue.
Actually, that controller won't support series connected panels - it's designed for parallel connections. The maximum input voltage from the panels is 25 volts and each panel is rated at 22.5 volts open circuit and 18.9 volts working voltage. Parallel connections add current while the voltage stays the same as a single panel. Series connections add voltage while keeping the current the same. Put two panels in series and you'll exceed the controller's input voltage.
When you connect the two 6 volt batteries in series, you've made a single 12 volt battery out of them. They'll charge just fine from the nominal 12 volt output coming from the controller.
The wire gauge from the panels to the controller is important, but more important is the gauge and length of the wiring from the
panels controller to the batteries. Mount the controller reasonably close to the batteries so there's not too much wire between them.
The battery charging voltage is set by the controller, and any voltage lost along the wires going to the batteries will reduce the charging rate as the batteries fill up.
The current shunt for the Bayite controller goes between the negative battery post and all of the wires connected to it.
One disadvantage of the Bayite is it only accumulates Amp-Hours in one direction. You can measure how many amp-hours you're putting into the battery but not how many come out so it's of limited use to determine the battery's state of charge.
What you really want is an amp-hour meter that counts up and down, up when the battery is charging, down when it's delivering power.
Victron BMV 700There's a different meter on Ebay, the 20 amp version with an internal shunt claims it will measure current and amp-hours in both directions, but that note is missing from the higher current models that use an external shunt. I'm waiting for a reply from the seller about this, if the higher current ones also measure current in both directions they'll be a much better choice than the Bayite