Trump is not a typical politician so I don't think he'll be as worried about maintaining a good relationship with the people in Congress as prior presidents did. Additionally, many in Congress spoke out against him during his campaign. They may go out of their way to make things difficult for him, or he might refuse to cooperate with them out of spite.
Although the Republicans control the House, the Senate and the Executive Branch that does not necessarily mean it is going to be smooth sailing for the Trump Administration. The members of Congress have a different constituency than the President and they will have different goals that will not from time to time comport with Mr. Trump's broader goals.
Congress has already shown that they will do whatever it takes to appease Trump.Throughout the entire election cycle, they stood by like a bunch of puppets, fearful of angering the Donald. They have already scrapped their plans over the ethics committee, and I believe Trump criticizing them had a lot to do with that.
No, Trump will not have a problem with Congress during his term. Republicans currently enjoy majorities in both the Senate and the House of Representatives. Like Trump, their main objectives are to transfer the remainder of the middle class's wealth to the rich, and dismantle the institutions that protect citizens and the environment.