Why does your accountant need copies of your checks? Are you being audited, or are you asking theoretically in case you are audited in the future? You don't have to submit any proof at the time of filing a return.
"My church doesn't send me a letter of the annual contributions."
Can you request one from them, or do they not keep a record for each person?
Checks and bank statements do serve as evidence. You can treat each check as a separate contribution.
If any check was $250 or more, however, you must have an acknowledgement from the charity/church for that donation, and there are certain other requirements, as explained in the record keeping section of this publication:
See IRS Pub. 526--Charitable Contributions.
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