I forgot the DS1302 has two supplies.
I would connect the DS1302 as shown here but use a diode with the battery, and have the trickle charger turned off. I do not have enough experience with the DS1302 to say about trusting it. http://www.maxim-ic.com/images/appno.../3449Fig02.pdf
A 1N914 woks for the diode.
Here is what I was getting at when I posted before. The whole system runs on 3.3 volts.
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