If I return to the gym a couple of times a week to do fundamentals (Squats, Cleans, Deadlifts and Bench) will I mess up my routines?

I signed up for Centr and it's been kicking my butt all week, I do at least one of the workouts they recommend a day off there, usually boxing; I've been coupling those workouts with a tight-quarters Navy EZ-Bar routine from Men's Health. I chose that routine because with school, appointments and family it's easier for me to do than trying to get to a gym every day.

Now that I'm back in it, feeling and seeing results, I want to get back in the gym twice a week to do fundamentals. I've heard a lot this week that certain exercises cancel out other exercises, I usually wouldn't believe that but it's got me worried.