Does it matter where you put the html javascrip for background movement and Mouse effects. How do you change how fast/the rate or what the image the javascript moving like moving object...and snowfall.
Can you use more than one background or and mouse effect at one time?

It all depends on the script. Any (decent) script should have precise instructions as to where it goes, or where the different parts of it go.

I can't imagine anything worse than mouse trails AND snowflakes

thats why i want to replace the falling snowflakes with a different image like a skull. And how do i add boarders to my website?

AS the previous response said, it depends on the script.

Borders - to achieve a solution that works for all browsers and all screen resolutions you will need to use tables. Depending of the effect you want either use the table borders themselves or use a graphic in a cell.