As noted previously, the problem isn't trademark, it's libel. You can certainly have a character eat at Wendy's or buy something at Wendy's or talk about a craving for a Wendy's product or whatever. You can even have a character who thinks Wendy's burgers aren't as tasty as McD's burgers. None of that is libel.
For something as major as the protagnist's job, though, I would suggest going with a fictional version of the company. The thing is, it's hard to tell what a company might consider libel. For example, let's say your story has a really horrible boss who engages in sexual harrassment. Now, it's unlikely that Wendy's will sue over that, but if they wanted to, the argument would be that the book portrays Wendy's as a company that condones sexual harrassment, which is libelous. And then there are even less clear cases -- let's say there's an employee who's just a jerk, or there's an employee who's an atheist or an employee who's a radical libertarian. Those would be even harder to prove as being libelous, but the cost of defending, even against a bogus claim, is substantial. (Oh, and don't forget, it's the AUTHOR who pays these defense costs. How much of a risk taker are you?)
So, me, I'm hugely risk-averse (part of my legal training), and presumably publishers (who listen to their lawyers) are too. So, where it's such a potentially major part of the story, and it's impossible to tell exactly what a major corporation would consider libelous, and it's expensive to defend a libel suit, I would recommend a fictional version of the workplace, unless you decide that all those risks are worth taking, because it's just that important to name names. In other words, if your whole point is an expose of Wendy's floor-mopping technique (or whatever), then of course you'll mention the real company, and make sure you've got your facts right. On the other hand, if the point is simply that the character is working a minimum wage job in the food industry, and is embarrassed -- not by the menial nature of the job, but by the ghastly commercials the company uses -- then it doesn't really matter if it's Wendy's or McD's or BK or something you made up.
JD, not giving individual legal advice, just general information