The question is im using a 3.7V battery of 3000mAh that is 3A per hour and if i use 2 in parallel would it be safe to power the board and not damage it?
You could have a "100,000mAh" battery, the device will only draw what it needs.
PE - the parallelling bit is a separate issue.
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As long as you connect the battery correctly to the board and the battery is of the correct voltage then no harm will come to it. The board will only take the current that it requires no matter what the battery may be able to deliver
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Think of it the same as your laptop/computer you plug it into a source that can provide maybe 100 times more current then required but like the Arduino it will only take what it needs assuming voltages stay within limit.