You are putting a LOT of points into that Hero. A LOT. I'd recommend you water him down some so you can have some points to throw around elsewhere. Granted, using the guy will be fun, but you'll benefit more from some bulky units of Marauders.
As for the kit, I'd recommend losing the Filth Mace, since at 1000pts, you won't find too many characters to make it worthwhile. The Necrotic Phylactry is nice, but is not too useful against the Empire (if only to auto-pass some of the spells that may come your way).
As for your Marauders, you're almost better off with Great Weapons. The initial +2S is nice, but in later rounds, you get hosed. Remember that if you start a combat using your Flail, you'll have to use it throughout the duration of the combat, so your shield won't benefit you (unless I am mistaken?). Light Armor and Shield will increase their survivability, but then they're starting to cost a bit more than they're really worth. After all, a charge from some Knightly Orders will obliterate just about all your armor save anyway, so you're better off with a higher S in protracted combat.
For your Hounds, I'd suggest a group of five per unit with the MoK. So, if you put your mounted Hero with your Knights, you'd probably only need a single unit of five. The rest can harry flanks and the like.
For Tactics with what you have now (WITHOUT MY IDEAS ABOVE), I'd recommend the following:
Your Marauders (with full command, yay!) and a unit of Hounds will hold up the Empire's stronger units (Knights, Greatswords, etc) with ease, but will take heavy losses. The hounds can hit their flanks and give you some extra combat resolution. Otherwise, just send them into the Hell that is an Empire Gunline. In any case, they act as a tar pit that may just win you a combat or two.
If you can charge your Marauders in, great. If not, they'll drop. Don't worry, it's what they're best at! They're cheap, and the Empire's real focus should be your Knights and your Hero. Your Marauders might just hit a flank.
Meanwhile, your Knights with your Character are restrained by a unit of hounds. That is, until the hounds are decimated by one of many terrible ways to die at the hands of the Empire. At which point, your scary Knights will be ready for the charge anyway. You're best bet is to use them in tandem with your Marauders, hitting the flanks of the Empire Knights, preferably.
Otherwise, your hero can go Cannon Hunting, while your Knights suck up some cannon balls. Hopefully, what is left of your knights will still deal some damage to the Empire units.
Cliffnotes: Your Marauders will hold the enemy, your Knights will deal the damage. Be wary of those Cannons and make sure you can get the charge!