The Duke was an Anglican, but he chose as tutor for his sons, Phillip, Thomas and William, a fine scholar called Gregory Martin, who had leanings toward Rome and was later ordained at Douai. His influence on the young men was profound, both in turning them towards the old faith, and in instilling a love of literature and scholarship. After a time at St. John's College, Cambridge, William and his wife lived in a home called "Mount Pleasant", at Enfield Chase, Middlesex, where their fifteen children were born.

Their pleasant life was interrupted, however, when William find himself in prison with his half-brother, Phillip. In 1583 Phillip declared himself a Roman Catholic and William soon followed his example. This immediately placed them in a dangerous position, as the Pope's excommunication of the Queen resulted in all Roman Catholics being regarded as treasonable. Both were imprisoned in the Tower on more than one occasion, and Phillip, who had planned to leave the country, eventually died there.

The Dacre family did not allow the estates to pass to the Howards peacefully. Elizabeth's uncles 'stomached it much that so goodly an inheritance descended by law to their nieces' and years of lawsuits resulted. It was not till 1601 that Elizabeth at last allowed them to receive their estates, and then only on a payment to the Crown of about £10,000 each. Soon afterwards William made his home in Cumberland, restoring the old Dacre fortress of Naworth.

In 1603 William and his Lady took up residence at Naworth Castle, Cumberland. Unlike many of the Howards, William had the reputation of a man of the highest character. He displayed sound judgment and brought his cultivated mind to the work of restoring order and furthering civilization in the wild districts of the borders. He greatly improved his estates, encouraged agriculture, and attempted to promote the well being of the people in general. His praise worthy efforts were not always appreciated by his neighbors, and many attempts were made to get him into trouble as a recusant; someone who refused to attend the services or recognize the authority of the Church of England. Because he was a Catholic, he was not permitted to hold any public position until 1618, when he was made one of the commissioners for the borders. He insisted on the due execution of the laws, and by his perseverance, he annoyed greatly the neighboring justices, but his proceedings were always in strict accordance with the law. He has been betrayed in "Lay of the Last Minstrel" as a mythical hero by the name of "Belted Will", but he was known in his day as "Bauld (bold) Willie", and his wife as "Bessie with the braid (broad) apron", meaning she had an ample behind.

William Howard was a scholar of note, a friend of Camden and Cotton and one of the little group who set up the short-lived Society of Antiquaries. He built up a large library, mainly of history and theology, was a pioneer in collecting Roman remains and edited a monastic chronicle. Camden described him as 'a singular lover of venerable antiquities and learned withal'. Lord Howard had begun to collect books very early in life, and he formed at Naworth a large library. When a proposal was made in 1617 to revive the Society of Antiquaries, which King James I had for some reason suppressed, a memorial in favor of the project places Lord Howard's name first in the list of its probably members. The couple also maintained a lovely garden. Living close to the Roman Wall, they collected Roman altars and inscriptions and placed them throughout the garden. Unfortunately, they are no longer found there, subsequently scatter or destroyed.

Elizabeth died in 1639 and a year later, when Naworth was endangered by a Scots army, the sick and aged man was taken by horse-litter to Greystoke, his sister-in-law's castle. He only lived a few days and was buried in Greystoke church. The families of two of his sons remained in the area at Naworth and Corby Castles, and are there to this day. The great-grandson who became the first Earl of Carlisle became an Anglican, as his family have remained, while the Corby branch has always been Roman Catholic.

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