From: Connecticut, USA
Interesting idea. I see what you're trying to do. Half a lifetime ago I used to use cardboard miniatures myself, mainly the old Avalon Hill games Bismark and Jutland. Even though I realize these games are probaby not as advanced as what you're doing, they're the basis of my answers below, so if I'm leaving something out that's obvious I apologize in advance.
Anyway, the simple answer is would be very difficult to do what you are prpososing with WPO. You'd basically have to become very adept at using the scenerio and database editors. Formulas would have devised so the damage taken by the miniatures could be reentered into the editors so the ships would show up proportionally damaged in WPO after the battle. Unfortunately, that would be easier part.
The much harder part would be trying to reenter all of the coordinates of all of the units, including their damage, fatigue etc., to reflect the conditions on the map which have changed from the start of the game to the end of your battle - for both sides. Once you had done that, would would in essence reload a new scenerio, and go from there. That, I'm sorry to say, will be near impossible if you're playing against the computer, and will require an enormous amount of trust and cooperation if you're playing against a human opponent.
The only way I can see this working with WPO would be a very limited scenerio - either one you developed or one of the smaller stock ones, like Pacific Jutland, and maybe limit the miniatures to the big naval battles rather then the skirmishes. WPO would probably be great to give you a good set-up to a big naval battle, but the follow-up afterward would be quite difficult to do.
If any other WPO player has a better, easier solution, hopefully they'll come forward - that's the best I can come up with. If you're new to WPO you may enjoy playing against the computer for now to learn the intricacies of the game, but maybe in the future you might want to give PBEM a try - it really brings out the game's best qualities! If you browse the currently active AAR which is going on right now elsewhere in the WPO forums, you can see that with the right opponent you won't suffer for lack of action!