Keep it simple. For donations, I'd just put everything for the week into a envelope, put the date on it, and file it that way.
For expenses, staple everything to the check request and file by check number.
Any membership stuff was filed chronologically. Takes longer to find, but really quick to file. Odds are you won't need to look things up too often.
Check the retention period for your country. For the US, it's 3 years plus current. So, you can shred anything before 2017.
Do keep a lookout for priesthood ordinations. There's a time when the church failed to record the "ordained by" information.
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