It sounds like what you want to do it to use the Chroma Key effect to create a clip with a transparent background, that can be stored with that transparency baked in to the clip and so simply imported and placed over the background of choice, is this correct?
I don't have FCE on the machine in front of me, and it is many years since I used it - so I am not sure what exact options are available for you but this is how it would be done in FCP-7:
Create a timeline that matches the source footage properties.
Place the clip you want to make have a transparent background on V2.
On V1, place a light background so that you can judge the clip on your key.
Put the Chroma Key effect on the clip on V2, make adjustments to get the clip as close to your liking as possible.
When you have the key set -
Remove the stand in background on V1 so that the clip on V2, with the effect applied, is now the only thing on the timeline.
DO NOT RENDER THIS! If you had rendered it to check clip over the fake background, it should have un-rendered when you removed the fake background. Remember, it must be un-rendered in your timeline for the following steps to work.
Select the sequence in the FCE browser, make sure there are no in or out marks on the sequence.
Go to the menu File > Export > Using Quicktime Conversion . . .
At the bottom of the Navigation Box that opens, next to the Format: drop down menu, you will see a button for Options.
Click that button.
When the Movie Settings Pane opens, click the button for Video size. If the size is not what you expect it to be, set it there from the list of choices and then click OK.
Now click on Video Settings.
When that window opens up, choose Compression type Animation from the drop down list, and set the Compressor (if it is not already switched to this setting) to Millions of Colors+ . The plus sign is critical, it is what will tell QuickTime to preserve the transparency.
Click OK.
Check you settings, if everything looks good then click OK.
Name the file and navigate to where you want the file stored and the click OK.
Once you click OK the file will be created with the transparent background.
To test, import the file you just made and test to see if the transparency has been maintained.
Depending on the horsepower of your computer, it is unlikely that you will be able to play this clip with transparent background without rendering first,
MtD