In Indesign you margins are you text frames... as in, you don't need to draw text boxes on you paster pages.
There are two way to go about this:
View>show frame edges
Set up you margins like you normally would on the master pages.
Draw text boxes where ever you want them to be on the master pages.
link them together (like in quark) by (black arrow tool) clicking once in the little blue box in the bottom right hand side of the first text frame then click again in the top lefthand little blue box of the second text frame to link them both together, etc etc. if there are any more...
goto page 1
so with you black arrow tool selected.
File>Place: (this will "load" your curser up with you text file)
Hover your curser over the first text frame you wish to put the text in. it should turn into a picture of a chain link (like in Quark). If you get that then hold down shift and simply click.
The other way is heaps better IMO.
Set up you master pages with you pink margins acting as text frames
so you may end up with 10 different master pages, each with different margin set ups i.e one for text with margins set to 10mmTop, 10mmBot, 10mmLeft, 10mmRight. And also one for Chapter heading with same margins as text except the top margin will have a drop of 50mm on it.
Then
File>Place to load your curser, hover your curser at the top left position of the margin, hold down shift and click...
I really hope this makes sense...
Master pages in InDesign compared with Quark are light years ahead in term of what you can achieve with them
All this is in the help files that come with indesign...
Good luck, happy InDesigning, let us know how this works out...or if you have any more questions...
Marcus