Placing images created in Photoshop of Fireworks removes their transparency - how to resolve?

I am designing a logo in Illustrator and have been using Photoshop and Fireworks to edit some photographs which form part of the logo. These photographs are basically of musical instruments and two lions and I've used the rubber tool in Photoshop/Fireworks to cut out the shape of the instrument/lion and leave a transparent background. I've then done a colour fill on the photograph so that it is a single solid colour shape. I save this file, either as a PSD or PNG, and then place it in Illustrator using File > Place.
However, when I cut and paste the logo from Illustrator into InDesign any images that I've been working on in Photoshop / Fireworks have suddenly lost the transparent background they had and instead are displayed as the single solid colour shape but surrounded by whitespace.
How do I resolve this? Should I be saving it a particular way in Illustrator in order to make all whitespace in the Illustration transparent? Or is File > Place the wrong way to import graphic elements?
Also, is there a way to colour fill the imported images? At present I have to jump back out to Photoshop to change the colour and then AI picks up on the save and updates the graphic - it would be nice if I could do that all within Illustrator.
Appreciate the advice. Thank you.
NJ

Sorry, completely new to Illustrator.
Let's start from the beginning...the background (page) of Illustrator is white. I can't seem to get it to be transparent so I'm assuming that white is the default and you should just know that it's transparent?
Anyway, I created a logo against this white backdrop. I then wanted some solid colour graphic elements (musical instruments and a coupe of lions) as part of the logo so I opened up some photographs I had of musical instruments in Photoshop, used the eraser tool to remove all but the instrument then did a colour fill on the remaining image so that I had a single colour fill instrument shape. I saved as .PSD.
In Illustrator I did a File > Place to insert the above graphics into my Illustrator logo design.
1) Is it possible to do this colour fill in Illustrator because at the moment any time I want to change the colour of the instrument of lion graphics I'm having to go into Photoshop, change the colour there, save, and then wait for Illustrator to update.
2) Rather than my "dumb" (how rude!) copy and paste procedure what is the best way to get the completed logo into InDesign? File > Place and select the Illustrator file?
Thank you Mylenium.
NJ

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