Credit to the Germans for at least realizing that a single carrier (see: Aquila) isn't much of a threat to anyone in-general, particularly when you're just diving into carrier warfare for the first time. The Germans didn't always have great ideas when it came to the Graf Zeppelin, but they at least paid attention to other nations' designs and tactics. In particular, Raeder seems to have taken a lot of interest in the pre-war drills run by the Americans with Lexington and Saratoga, and really did plan on running two carriers under the 'Z' plan- but not together. Rather they'd have operated (in a perfect world) as the centerpiece of forces consisting of a couple of battleships and other escorts, providing cover and scout support and adding in some firepower while the battleships did their jobs.
Whether it would have worked is anyone's guess- like the Italians, the Germans had no experience with sea-based aviation and were kind of winging it (pardon the pun), so how well the navalized Ju-87s and such would have done in combat is tough to say. Either way, Hitler's impatience ruined the Kriegsmarine's plans before most of the ships planned were ready anyway. Worth considering though... if there's a few navalized Bf-109s flying around overhead when Ark Royal's planes arrive, might Bismarck have made it to occupied France for her repairs rather than taking the fatal torpedo?