1. Employ a defensive midfielder
I mean a real defensive midfielder, a link between the midfield and defence. This guy is going to man-mark the opposing main AMC and play him out of the match. Or try to anyway. He's supposed to disrupt the attacking build-up from the opposition.
2. Remove all closing down from the centre-backs
The centre-backs are often drawn out of position because they close down an opposing midfielder, leaving the defence prone to a through-ball through the centre. Just have the defenders stand off, the opposing players will run at them and are usually easily muscled off the ball in such cases.
3. Push up the defensive line
Limit the time and space for their AMC's to move in. Basically make it harder for these guys to play their beloved counter-play by either catching them off-side or limiting their passing options by clogging up the centre of the pitch.
4. Harass their defence
When the centre of the pitch is congested, these AMC's rely on a a proper build-up from the back. When you pressure their defenders and mostly their wingbacks into lumping the ball forward, your defenders usually beat their AMC's in the air and win the ball back for you.
Now please note that these tips are not a sure-fire way to beat a 4-6-0. You obviously need a decent tactic of your own and the right players to execute it, but it should help you to get an edge over the opposition. I actually win 80%of my encounters with a 4-6-0 these days.