Your run time should double if both batteries are in the same condition and deliver the same number of amp hours. Even if you have one new battery and another that's on its last leg, you can get the most out of two batteries by using them independently. What you want to avoid is having a strong battery depleted in its attempt to maintain the charge in the weaker battery. You want all the amps delivered to your TM.

Most of my trips are TMO lakes, so I'm totally dependent on my electrical system. I run my older (weaker) battery until lunchtime and then switch batteries for the afternoon. Yes, top speed drops as the battery delivers its amps. If it's important to maintain a constant trolling speed, I advance the power setting (actually, my iPilot does that automatically with the Cruise Control feature.)

When the morning battery is drawn down close to the danger level or at lunchtime (whichever comes first) I switch to battery #2 (the newer one.) If conditions are really tough in the afternoon I can always reconnect the morning battery and draw it down deeper in order to continue fishing and make it back to the dock.

Since my batteries are drawn down to the same level (more or less) I get the shortest recharge cycle. If I were to run one battery all day and draw it WAY down, recharge would take longer and the battery might be damaged--shortening its service lifetime.