This link may help you understand the combat system:
http://www.ageod.net/agewiki/Combat_Explained
"How do you enter an area that has an enemy stack in it without attacking? Every time I go into an area with an enemy stack I always have to attack."
Well that is the whole point really. Unless the enemy stack consists of cavalry set to Green/Green and evade combat, then you are going to detect them and attack. However, you can apparently lose a battle and remain in the same region with an enemy force under the new rule.
I have had some success moving an army set to Conservative Attack (Blue/Orange). The army attacked at a slower pace allowing three Corps stacks enough time to MTSG, delivering a crushing blow.
"Also, what is the ratio for a successful victory when you attack an equally good army that is numerically equal to mine?"
I'm a strong proponent of superior quality versus quantity. You can't always pick which units must defend against an attack, but you always choose which of your units you use to launch your own attack. A well commanded stack with Infantry Divisions consisting of a marine/sailor, a sharpshooter, a cohesion boosting brigade and the rest line infantry, supported by an artillery Division of your best guns is just going to do better than a numerically equal stack of lesser troops poorly organized.
"In big battles, have any of you won a battle with lower numbers and less General leader superiority when you were on offence?"
In a battle for Richmond, Grant did the Conservative Attack at pretty bad initial odds, then was reinforced to win the day. So I was out-numbered, but not out "Generaled". Of course, you can use the battle-planner feature to gain an advantage, too.
"The reason I ask this question is because right now in the game I am currently playing I have the AI on aggressive but they didn't come to me at manassas. They just sit there in Alexandria, usually till mid 1862. One game they stayed there till 1864 and finally hit me like a mac truck and there was nothing I could do, what am I missing here."
The CSA player has two options. The "play so you don't lose" strategy and the "play to win" strategy. Although I can put up a pretty good defense, I much prefer going after Wahington D.C. The Union players and Athena don't defend their capital very well.
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After the first Bull Run, Davis sent orders to march on Washington, but the army was too disorganized chasing fleeing Yankees. Right from the first turn, build an army to take D.C. and do whatever it takes to make that happen as soon as possible.
Otherwise, use stockade and redoubt RGDs, forts you construct from artillery and supply units and natural barriers like rivers to build a linear defense supported by your best army in reserve led by Lee. I've seen too many AARs with Corps stacks spread out like an egg shell, as though MTSG happens automatically. A Division in a stockade/redoubt/fort can stop an army's advance. A line of these allows more of your army to be in the reserve for your counter-thrust.
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"How would you recreate a real battle like Chancellorsville?"
The battle planner feature might occasionally recreate something like this against Athena. Otherwise, you would need a Union player to be incompetent.
Paraphrasing Clausewitz, when a great General uses a flanking maneuver to win a battle he is praised. Not because this is a great accomplishment, because the lowest lieutenant should know how to do this. The General must ignore a thousand distractions, focus on what matters most and force his will to do this to the exclusion of anything else.
Good luck!
P.S. I did this once but it is complicated and dangerous:
This is an application of infiltration, where you sneak into a defended position. The enemy has a series of strongpoints along a river line. The player will suffer a considerable disadvantage to move a large army across the river and attack. So take one Division with a 2-star Corps commander and brake the unit down into 4-5 small groups of 4 elements set to Green/Green, evade combat. This gives each brigade group a high Evasion value and Hide number. Then move the small brigades across the river without the need to switch to Offensive posture. The Cavalry Screen RGD will add to their Hide number. Finally, reconstitute the Division the next turn and further make it a Corps under the 2-star. If the enemy doesn't have 100% MC in the region, then this Corps can dig in and get reinforced with each new turn until you have a complete advantage. If the MC is 100% for the enemy, then your unit will be switched to Offensive mode. No problem, set the "Corps" to Conservative attack (Blue/Orange). This should give them a slow paced attack allowing the rest of the army to March to the Sound of the Guns and thus get no penalty to cross the river.
I'm the 51st shade of gray. Eat, pray, Charge!