Whether you do $100 a month or save up and deposit $1,200 after a year, it is still 0.35% of assets under management (as long as you deposit at least $100 a month). Just create the account now and start making your monthly contributions. Just make sure you continue adding $100 a month or that $3 fee will eat into your returns.
One thing I've mentioned to friends and family when referring them to Betterment...it doesn't have to be $100 all at once. If you get paid twice a month, you could do $50 each payday. If you get paid every 2 weeks, then you can do $50 every 2 weeks which is an average of $108.33 a month. For some people who aren't used to investing and have a tight budget, splitting it up helps them out.