I recently purchased a BassPro XPS 4/4 onboard charger; the one with two-4amp connectors. The manual says to connect one set of wires to the starting battery & the other to the trolling motor battery. I've got a small outboard and am not concerned with charging the starting battery. Can I connect both cables to the trolling motor battery--two reds to the positive & both blacks to the negative?

No. Only connect one set to the trolling motor battery.  Why wouldn't want to charge your cranking battery too?

Sometimes I fish consecutive days and want the trolling motor battery fully charged. The motor charges the starting battery enough, and if worse comes to worse it pull starts easily. 

I guess since it's only 4 amps per bank you could hook both up and not hurt the battery but according to Minn Kota's website.

 

this will charge the battery almost twice as fast. However, the water in the battery is more likely to evaporate with higher charging currents. Thus, the electrolyte level should be checked more often. The maximum safe charging current on a regular battery is 20 amps.

You mentioned that your motor charges the start battery. Unless you run for several hours each time out, your battery is not being fully charged. Not sure if you run electronics, live well pumps all day, etc.. but if so, its just a matter of time until you end up stranded. Where are you fishing--Lake Ashbaugh, Lake Charles or one of the many rivers in NE Arkansas (Black, Eleven Point, Spring, St. Francis)???

 

Some chargers charge differently than others and can harm your batteries if you hook it up that way. That being said, I owned a 3 bank 5 AMPs per bank XPS charger that had a bank go out while under warranty. BP did replace it with an identical charger that also quit while under warranty. I tired to take it back and get a refund, but all they wanted to do was replace that one. I broke down and spent nearly $300 on a NOCO Gen 3 charger which has 10 AMPs per bank. It has all kinds of sensors to avoid over charging that will damage your batteries. When a battery is fully charged, it will automatically switch that load to another lead which will charge that battery faster. If for some reason the leads get crossed or the battery has an internal short, it will shut down that bank. When battery is fully charged it goes into a maintenance mode to keep the batteries charged. Some boat manufacturers are now putting in NOCOs as standard equipment. I've had mine for 4 years now without a single problem. AND I just replaced one of my TM batteries a month ago. When I pulled it out I discovered that April 2013 was the purchase date. I have used the same battery brand for many years but have never had one to last more than 2-2 1/2 years. I attribute this to the NOCO charger. It may be a little more expensive than some, and by no means a top of the line charger. If it is making my batteries last twice as long, over the course of 4-5 years, it actually pays for itself.