I'm referring to the two times when Marco hums the song to himself whilst on a scam-mission, just before he's approached by Jimmy and their unsuspecting victim. The second time, he doesn't complete the bar and instead is interrupted by his cough, but if you listen closely you can hear he finishes the bar with "cough-beats" not in tune obviously but in the correct rhythm.
I believe smoke and coughing are associated with death, and if you've seen the series (or read the opening line of this post) you'll know that Marco dies shortly after the coughing. However I've noticed with Vince Gilligan's work, there are so many hidden meanings behind certain details that would otherwise seem irrelevant to someone who isn't fully engaged in the series.
I believe there may be some deeper foreshadowing here. Maybe "Smoke on the Water" is code for death on the horizon and possibly the song will come back in a later episode accompanied by a major turn of events?
Edit: Just watched the episode in the end and I was intrigued to see how Saul mimics Marco's actions, just after he tells Mike, "It's not stopping me anymore" meaning "The matter of fairness, justice and 'doing the right thing'" will no longer stop him. It seems like this way-point in the plot is where Jimmy McGill, a lawyer you can trust becomes Saul Goodman, a "criminal" lawyer.
Second Edit: After watching the series further, I found another couple references to the song. First when Saul is talking to his UNM film crew, he references 'Another Brick in the Wall' by Pink Floyd, the microphone man exclaims: "Deep Purple!" and then Saul says "This generation is doomed"
And again, after he banks a few commercials with the guitar shop, he's laying on the ground in between shifts of community service, playing the guitar and after a discussion with Kim about operating for the following 6 weeks, Saul plays the classic riff...