You will want to update the code where it displays the number... The eCart itself has settings where the currency format can be changed... If you edit the cart object in dreamweaver it will be on the first screen.
Sometimes we use the number_format() function as well... in those cases you might want to do a site-wide find for: number_format(
then wherever the function is used add two parameters to reset the decimal and thousands separator like: number_format($value,2,',','.')
You could also just add the number_format function to reformat it outside of the cart as well.