Travel between the Heartland's major cities is easy; distances are (relatively) short. Even if you only have a few days, you'll still be able to see a lot.
If you have 3 days. Fly into and out of León's airport and base yourself in Guanajuato, enjoying its spectacular architecture, silver mine and church, and memorable funicular ride. Visit San Miguel de Allende on a day trip; it's an easy 1½-hour drive from Guanajuato. Alternatively, fly into Querétaro, visiting the Sierra Gorda missions and Xilitla, and make a day trip to San Miguel.
If you have 5-6 days. Spend the first two nights in Guanajuato, and the third night in San Miguel. Next, head south for a few hours and staying in the bustling university town of Morelia. From there, it's only an hour drive on a superhighway to Pátzcuaro, which for many people is the highlight of the Heartland. On your last day, take a boat ride on Lake Pátzcuaro. Fly back out of Morelia's airport, which is nearby. An alternative route would begin by flying into Zacatecas and spending two nights there, then driving down to Guanajuato and spending the balance of your time there and in San Miguel.