Trump couldn't overturn marriage equality even if he wanted to. But the Republican controlled Congress and Senate could. Then the human and civil rights groups would have to file a case against the law. The case would have to work it's way back up to the Supreme Court and then if Trump picks the next Supreme Court justice that individual could be counted on to vote against marriage equality, as Trump has said he will only nominate the most conservative judges.
Again, with the ACA, it is the same situation. Trump cannot cancel Obamacare. While he could sign an executive order, it would be immediately challenged in court and the order would most likely be stayed at least temporarily. Congress and the Senate can repeal the Affordable Care Act and then Trump signs the new law. I suggest checking out Paul Ryan's plans to end Medicare.
http://www.salon.com/2016/11/15/paul-ry ... is-moment/
So long as Trump keeps signing the laws that conservative Republicans in Congress want passed (repeal Obamacare, privatize Social Security, overturn campaign finance and environmental regulations, etc.) they most likely will not interfere with the things that DO fall under his purview.
Checks and balances don't work when one group is in control of all the levers of power.