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The backup battery is a separate physical battery from the main battery, and it recharges when the Ipaq is connected to a charger.
The problem is that the backup battery is only intended to maintain RAM data while you remove and replace the main battery so it has a limited capacity (in my experiments with a new 2215 the backup kept the RAM intact for about 30 minutes with the main battery removed before the unit went to hard reset).
Because of this limitation, HP added an option that allows you to reserve a selected fraction of the main battery to keep the RAM alive for a longer period should your charge reach a user selected level. This allows those who use their Ipaqs in environments where they can't quickly recharge if the battery gets low to insure that they won't lose their RAM before they can replace the charge.
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