Ask the commercial printer what PDF preset he would like you to use in InDesign.
There are multiple print workflows: Some printers have no problem accepting PDFs with RGB images with embedded profiles. They tend to have to newest equipment. Those commercial printers may want you to use the PDF/X-4 preset which would preserve the RGB profiles in your project. In general, that would produce the best result. (For example, a lot of progressive printers use Adobe PDF Engine RIPs for which this is true.)
Other commercial printers have older PostScript processors. They will want you to convert RGB to CMYK, and to flatten transparency. They may ask you to use the PDF/X-1 profile. This will do the conversion for you, and discard the RGB profiles.
Best answer: Get more information from the printer.
And to add to Steve's reply, check with your printer before you start laying out pages, what is an economical page size and extent (the number of pages that are printing in a section).
If I need to convert all to one or the other do I need to do this as a batch process in Photoshop or can this be done in InDesign?
You don't have to get all of the placed RGB images into a single color space as long as your document's RGB CM policy is set to Preserve Embedded and the images have embedded profiles. In that case when you export to PDF you can include all profiles via PDF/X-4 (as Steve suggests) and let the printer make the conversion to CMYK at output. Or, if you need to provide an all CMYK document you can set the destination to the print CMYK profile in the Export Output tab.
There would be no benefit in batch converting to a single space in Photoshop—something like sRGB-to-AdobeRGB-to-DestinationCMYK wouldn't produce a better result than sRGB-to-DestinationCMYK at Export.
If you need to color correct the sRGB images it might be beneficial to convert to AdobeRGB first because its gamut is larger than sRGB's
Thanks to all for your help. It is very much appreciated. I'll ask the printer ASAP.
Cheers for the info,