>Do I have to set Indesign up any special way so that when it goes to the printers it will know this.
Maybe. How is it going to be printed? Have you talked to the printer about it?
>Can I have black and white masters and colour masters in the one document?
In a sense, yes. ALL pages in ID are color pages, but you can certainly set up masters where the only color used is Black.
>Do I need to gray scale all my (black and white images) in Photoshop first?
InDesign CS6 introduced export to grayscale PDFs, but that turns everything in the PDF to grayscale so you would need to export your color pages separately from the grayscale pages, then recombine in Acrobat pro, or send to the printer in separate files. You also need to set your Appearance of Black settings (in the prefs) to Output All Blacks as Rich Blacks if you are going to export to grayscale or your black type will be screened to a dark gray. Personally, I'd do the conversions in Photoshop so you can see and control what is going to happen and avoid the export hassles.
Grayscale content is output in the K channel of the InDesign file, and your screen preview may not be accurate unless you use overprint preview.
>Do I need to do anything to the text to make it print in Black and white if I am using a black coloured font?
Your text will print in whatever color is you choose for it. If you use the default [Black] swatch, it will output using only black ink.