Create a new PS document at a square pixel frame size.
Recommended:
1920x1080 for HD projects (ATSC)
720x540 for SD project (NTSC or PAL)
Place your logo in the PS canvas over a transparent background and scale it such that it appears as you would like it to appear when superimposed over your video in FCP.
Optional: Apply Filter > Sharpen > Unsharp Mask to bring some sharpness back to the artwork after scaling it down, if needed.
Save the PS file as a PSD.
For import into FCP, save the file as a PNG (24 bit, not 8 bit). If your PS file has more than one layer, be sure to set your layer visibility as you would like the image to appear in FCP before you save it. Saving a multi-layer PSD as a PNG results in one merged layer in the PNG file. Also, add something to the file name that indicates that this is version one of the logo (like "_v1.png" at the end of the file name).
Optional: Open the PNG file and change the image size to match your Sequence frame size and resave the PNG.
As far as file formats go:
PSD - I usually save the PSD file as the master design file.
PNG - I usually save a PNG from the PSD as the file for FCP. It has built-in transparancy. If you can see the transparaent background in PS, you can see through it when superimposed in FCP as a PNG. Also, if revisions are needed later, I can save version two, three, four, etc.
JPG - I only use this for sending samples to clients to review. Although, it's fine for FCP if you don't need transparency as the JPEG format does not support either layer transparency nor an alpha channel.
-Warren