Run Thrash. It's one of the best Dark moves available, and the move you'll be using most often since it has 150 BP.
From there your (Hustled 80% accurate) options of Physical moves are Brick Break, Fire Punch, Poison Jab, Steel Wing, Strength, Superpower, and Thunderpunch. Your coverage moves should be used only if they will outdamage Thrash.
Breaking it down further with numbers:
Brick Break (75 BP) - Removes screens, but only half as powerful as Thrash
Fire Punch (112.5 BP): Physical Fire STAB
Poison Jab (80 BP): Kills Waters and Natures
Steel Wing (75 BP): Pretty okay neutral move, only really used for other Darks though
Strength (80 BP): Carries a slight chance to raise Attack and hits slightly harder than Brick Break
Superpower (120 BP): The "I hate Steel and Heart types" route, but will force switching out
Thunderpunch (75 BP): Use Poison Jab.
For the special move, the only things I can recommend are Blast Burn and Fire Blast, probably Blast Burn. Flamethrower is also okay if you absolutely do not want to miss. Keep in mind when using Flandre that you will miss important attacks and they will cost you Battle Tower streaks.
Anyway, Thrash/(Dream move)/Poison Jab/Blast Burn is probably what I'd run if I wasn't too afraid of missing every move.