Not exactly. The government's theory is that Cohen made an illegal contribution by spending personal money beyond specified limits to help the campaign. Where Trump got the funds to pay him back is irrelevant to that crime (although it could represent a second, independent, crime, if he stole those funds from his own campaign).
For those who want to implicate Trump in Cohen's crime, the key is that Cohen did this at Trump's direction. Whether or not Trump knew that he was directing Cohen to commit a crime is irrelevant (ignorance of fact can be a defense; ignorance of law cannot be). I find it very unlikely that a federal grand jury will ever issue an indictment of Donald Trump for conspiracy to commit campaign finance violations on these apparent facts, but if you want to know how the legal dots connect, there it is.