The modern evanjellybean lexicon is chock full of worthless jargon, and few phrases approach the utter worthlessness of "don't put God in a box". The easy route is to sneer that it's impossible, that God will do what He wants and we can't stay His hand, etc. True enough. But what is the cliché intended to mean?
It could mean that God does not fit our neat systematic categories. God is transcendent and awesome, and no simple statement or summary can totally describe Him or His works. Which wouldn't be the worst thing you could say, I guess. But it seems that usually it's taken a step further - that we can't say categorically who God is or what He will do. Por example:
Some say salvation is only through Jesus. Don't put God in a box!
Some say miraculous/attestational gifts ceased. Don't put God in a box!
Some people think God is sovereign in election. Don't put God in a box!
People put God in a box and think the Bible is the only way we find God's word.
Some people say God cannot lie. Don't put God... er, wait...
And so on. The cliché is not usually a warning against over-systematizing or reductionism, but a worthless (or anti-worthfull) shot against certainty in what God has revealed.
It's not 'putting God in a box' to believe He will do what He says He will do. It's not 'putting God in a box' to believe God is who He says He is. Interestingly, the Bible is full of commands about and case studies in taking God at His word, and not once does it refer to it as 'putting God in a box'. Do you know what the Bible pert near always calls this nefarious act? FAITH!
So to summarize, if "putting God in a box" means believing God has revealed truth that we can know and believe, then it's the heart of Christianity. By all means, 'put God in a box', if that 'box' is the truth He has made known to us.
5 hours ago