Use of tactical Vs. historic, role play armies

Manipular involving phalanx? How does that work?

The same as with Roman infantry, except instead of Hastati in front with a unit space between them, and Principes in the second row positioned in the spaces between the Hastati...you have your phalanx in front with a unit space between, and the Bastarnae in the second row filling the gaps. Any unit that enters the gap between your phalanx, gets whacked by the Bastarnae in the flank. Once holes begin to appear along the enemy front, you can roll up a line with your Bastarnae and continual flank attacks. However...you must not expose the Bastarnae to a flank attack, in turn, so you have to pay attention to where enemy cavalry units are.

Now the enemy flanks with cav, and actually charges them in at my battle line instead of my missile units

You need to place your cavalry to the flanks somewhat ahead of your main battle line, and you need to be aggressive with them. When enemy cav are attempting to flank, it's obvious way ahead of time. Move your cav forward to intercept. Break their line but don't give chase. Instead pull back to nearly their original starting position and wait to see how the battle is unfolding. Often times those broken cav units rally and return to try again...and you repeat the previous maneuver. Smash them but don't give chase. This is why I suggested 6 units of Greek Cavalry...you can rotate the attacking units while resting the others.

My brother won't train Greek Cav, only Militia

Militia Cavalry certainly have their place. But they are weaker than Greek Cavalry, and are worthless as an anti-cav unit. They have no armor and use a short sword as their secondary weapon, whereas Greek Cavalry do have some armor and are armed with a spear...the prime anti-cavalry weapon.