The Battle of Pavia (1525) really was the zenith for the Zwiehander, and by the 1560's they were fairly well gone, except for as Parade pieces, and there is a similar ebb in two handed swords overall (the Zwiehander usually being associated with a specific *design* of these class of weapons, specifically having the flukes above the ricasso, and more developed quillons and port rings).
As far as *where* the Zwiehander specifically, (and the two handed sword in General), is deployed, many Landsknecht re-enactors describe the Doppelsoldier armed with Zwiehanders as "shock troops". This does not appear do be the case.
Most often they are deployed with Halberdiers to guard the Ensign, or flag-bearer. They are usually placed in the center of the formation, so are a last-ditch defence for the Captain and Flag. They *can* get used in the manner described (charging down the pike ranks), but since their numbers are so small (1/2-1% of the Soldiers), it's not their normal task, to be sure.
As I have little contemporary written evidence, I can only judge by a few snippets of text, and then the contemporary pictorial evidence:
'Giacomo DiGrassi, His True Art Of Defence'
Translated By I.G., 1594
"The two hand Sword, as it is used now a daies being fower handfulls in the handle, or more, having also the great crosse, was found out, to the end it should be handled one to one at an equall match, as other weapons, of which I have in treated. But because one may with it (as a galleon, among many gallies) resist many Swordes, or other weapons: Therefore in the warres, it is used to be placed neere unto the Ensigne or Auncient, for the defence thereof, because, being of it selfe hable to contend with manie, it may the better safeguard the same."
'Certain Discourses Concerning Formes And Effects Of Weapons'
Sir John Smythe, 1590.
(In reference to how the Imperial forces are drawn up)
"When the great Princes of Germanie...are disposed to make warre...being bound (as they are) by their tenure Militarie to the Empire, some to find horsemen, and others to finde footmen at their own charges...form their regiments of footmen into great bands of 500 to an Ensigne... ...their milicia consisting of Harquebuziers, Piquers, and some Halbarders, with a few slath swords for the gard of their Ensignes..."
('Slath' sword is a euphemism for a two handed sword. I recently acquired a Catalog from the Landeshaus Graz that was printed in the 60's, and two of their two-handed blades are described as something like 'slather schwert' (sp? I'll dig up the book later)
quoted from: http://www.myarmoury.com/talk/viewtopic.php?t=4221