1080i footage not exporting right...

Hello to all...
I am working with FCP 5.4 still. I am starting a new video driven website and I am planning on using Adobe flash and Adobe Encoder to compress for the video's. Here's my situation:
Been shooting with the Canon XL2 at 30p to start with. I have compressed the video in many different ways but not getting a decent result that I would see with let's say tut's on the cow or www.hulu.com and several other site's. So what I don't know is, will the quality be better if I shot in HDV? I have a Sony HDR-FX1. I would be more willing to use the HDV but whenever I export it from FCP it never looks right. It imports fine into FCP but when I finish and try to export it out it looks all squished, and yes I thought it was exporting in 720x486, so I changed settings but then it still did the same thing. I shot in widescreen on the camera, imported fine, but exported all pushed together again. Tried many of the different setting's from the drop down menu but it never come out right. Sometimes it exports with black lines showing how it was compressed into a SD size setting. Also I sometimes pull the footage into AE and it shows the interlace. Is there anyone who can guide me on this so I don't feel so super stupid. I thought I knew FCP but it has definitely got the best of me.

Thanks
Chuck Obie