Why are my Tritone colors faded?

Hello,
I just taught myself how to convert an RGB image to a TRITONE image, but the TRITONE colors look faded (the 2 PMS colors, not the black). Please tell me what I did wrong.
This is what I did...
Image > Mode > Grayscale
Image > Mode > Duotone
Selected black ink & 2 PMS colors
Image > Mode > Multichannel
Erased the parts of each channel where I didn't want that color
And here are two further questions...
1. Converting to Duotone forced me to flatten the image. What if I want to quickly edit the image again? Is there anyway to preserve my layers so I don't have to go back to an earlier saved version and convert to Duotone all over again?
2. What format should I save the file in if I want to import it into InDesign? I was told "DCS file (Single File with Color Composite)," but can I also use TIFF or even PSD?
Thanks,
Pablo

I think I just figured out part of my problem. I was converting my color text to grayscale, so it became gray and not black, and that's why it looked faded when I converted it to TRITONE.
Now I can create a TRITONE image that looks correct in Photoshop, but still looks a little faded when I import it into InDesign and then export it as a PDF.
Could this be because I didn't save it in the proper Photoshop file format?
Photoshop only gives me 4 file format options to save in, and InDesign CS4 only accepts one, .EPS
Otherwise I got the error, "This files uses an unsupported color space."
However, there are several .EPS options. I chose "Single File with Color Composite".

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