(FORTUNE Magazine) – Carly Fiorina seems to have won the bitter proxy battle over Hewlett-Packard's merger with Compaq, but one small point remains. The war to make the combined company a success isn't over. It is merely shifting to new fronts.

The most urgent campaign: Win back the confidence of HP's employees. Dissident director Walter Hewlett claims 66% of shareholders in HP's 401(k) plan voted against the merger. The depth of anger reflects a corporate hangover from the elation that greeted Fiorina when she arrived almost three years ago. When business slowed and her promises didn't materialize quickly, employees felt betrayed. Hewlett's opposition to the merger catalyzed an atmosphere of near revolt. But HP has a long tradition of pulling together in the wake of tough decisions, and early signs suggest it could happen again. Even Hewlett, who has filed suit in Delaware contesting the way in which HP solicited votes, has made noises about supporting Fiorina if the vote is certified.

Carly may have a secret weapon in the fight to win over employees: Compaq CEO Mike Capellas, president and chief operating officer of the combined company. He is battle-hardened after helping integrate Digital Equipment with Compaq, and popular within the ranks. He may be able to soothe employee relations while Fiorina focuses on customers, strategy, and marketing--her real strengths. Says Tony Scott, chief technology officer for General Motors, a big customer of both companies: "Capellas is a dynamo. He will earn the respect of people inside HP very quickly."

Then there's the next front: integrating the companies. "The risk is the amount of time it takes," says Microsoft President Rick Belluzzo, a former HP top manager. "Salespeople will have to spend a lot of time explaining to customers what stays and what goes. That doesn't help sell more things to them. The question is whether you can maintain revenue during the transition." On the plus side, many customers like GM look forward to dealing with HP and Compaq as one entity. Says GM's Scott: "It eliminates complexity." Already 1,200 employees from HP and Compaq are working in so-called clean rooms on issues such as which products to drop, which salespeople should call on which customers, how to launch an integrated payroll system, and whom to lay off. Still, it won't be easy. Says one departed Compaq veteran: "The merged company is in for two years of guerrilla warfare."

The final front of the war is a strategic battle: how to handle services. In markets like PCs, Intel-based servers, and printers, the combined company will be No. 1, but its services lineup is lacking. Both sides have low-end maintenance and support operations but not the high-margin consulting and systems integration businesses that pull in product sales and could allow HP to compete directly with IBM, as Capellas and Fiorina promise. Some observers predict HP will closely align with a big technology consulting firm, possibly Accenture. (Compaq is particularly close to the Andersen spinoff.)

Ultimately, Fiorina's agonizingly public war could turn out to be the biggest win of all. In months of headlines and expensive ad campaigns about the vote, both sides agreed on one thing--HP is a precious and wonderful company. Yet one of HP's historical weaknesses has been a milquetoast quality--something about the company made it easy to ignore. The fight jolted the company from its complacency. Now, if the new HP can protect its vulnerable flanks, it might still win this war.