You'd better make your work in a reasonably wide mode but keeping an eye in the most likely output ways. That is: You'd better work with a reasonable editing RGB space but you have to visualize (softproof) constantly what you are doing in the kind of colour you're going to print at the end. So, if have pictures in Adobe RGB or sRGB for a litho offset job in coated paper that is best described with... lets say SWOP Coated blah. blah... You work the picturtes in that RGB space but you softproof your work with that particular CMYK color space before converting anything. And nowadays you usually convert only if your printer gives you the OK to use that CMYK profile to make a ready for print PDF. All this said taking for granted you are working in a reasonably decent screen that has been calibrated with some kind of colorimetre (and they are cheap enough. If you don't have one, go get it).
Forget about vibrant colors and what you see in screen. WYSIWYG is a myth in this sense. You've to think What I See Is What Is Will Print (As Crappy As It Might Be). Some print modes are good (coated offset) and some are ****** (newsprint). Such is printing life. The sooner you realize your limits the better results you'll get with the tools at hand.
InDesign is ready to deal with documents that have pieces in some different color spaces. No trouble... as long as you view them all in the same softproof mode... You'll be using the One Ring of the Proper Viewing Space.
Special inks (Pantone spot colors) are a powerful tool but they can be used only when the budget and the printing conditions make that use sensible. Use them sparingly but without fear, show your colours then.
If you are using a mixed color spaces document with many pages (InDesign typical situation), you convert everything just at the end when makin the final PDF... Unless you have some special pictures or pieces you want to deal with special care. Then you make by hand conversion taking extracare no to lose anything you want to keep. It's a question of workflow: Labour time against quality in balance.
If you have to convert images, that is done in Photoshop with, as I said, the proper use of spftproffing. You may find, for instance, in a situation where you prefer to lose some tones in the blues to keep some shades in a red robe... But there is masking for that as well.
Lots of things to learn in this trade. Welcome to hell ;P
Gustavo (Posting from quite sunny Madrid)
What books have you read so far? Once you establish a calibrated workflow including a proofer; you won't be so confused. A good rule-of-thumb is to speak with the print vendor before creating your document. They will tell you what files they accept in which color mode using a particular profile. I produce print files and always convert from RGB to CMYK; all the while maintaining a profile honor system in the file itself. 99% of the printers I've dealt with over 30+ years want the file in CMYK. If you are adjusting color percentages "by eye"; you're on the road to doomsville. I suspect the reason you have so many questions is because you continue to get bad information. Unfortunately, there are not too many reliable educational resources available to learn the complexities of Graphic Arts technologies. I recommend looking into Adobe's "Print Publishing Guide" as a start.