Good afternoon- sorry you’re experiencing unexpected guests in your garden! First of all, do not attempt to trap and relocate the chipmunks. 
The most effective and harm free method of controlling chipmunks would be exclusion. Can you install short fencing or hardware cloth around the garden space in a way that would keep them out? There are repellants available but close attention should be paid for the labels and recommended uses. 
Also definitely make sure you don’t have any low hanging fruit as far as pet food or bird seed, etc available at the chipmunks level that might encourage them to stay! 

Hopefully this all helps- below are a few good sources to help you learn their behaviors and habits and find a method that works for you and your small guests! 

https://www.maine.gov/dacf/php/gotpests/othercritters/factsheets/chipmunks-penn.pdf

https://www.maine.gov/dacf/php/gotpests/othercritters/factsheets/chipmunk-purdue.pdf

https://www.maine.gov/dacf/php/gotpests/othercritters/factsheets/chipmunk-vt.pdf