I think remember Hugo saying the big cap (is it a super cap?) should last up to 2 weeks keeping the RTC going. This should charge almost immediately after turning the unit on so there's no need to "give it a good charge" as you would a car battery.
For the record, I recently went overseas for 15 days with my empeg powered off and the RTC kept time fine. And yes although I left it in the sled in my car, I had disconnected the -ve battery terminal (for other completely unrelated reasons)
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Christian
#40104192 120Gb (no longer in my E36 M3, won't fit the E46 M3)