I have a website that sells Jewish music Cd’s & downloads. Customers can buy, either CD’s that are shipped after shabbats, or download a song instantly. However, the money from the credit cards is not transfered to my account until I physically put it into my account, on Monday. Is this allowed? If someone acceses the site, say in California when its still a weekday by them, are they creating a problem for me? Actually, its always not shabbat somewhere in the world. Would I be allowed to leave the website on for those customers & not have to be concerned for the Mechalei Shabbat?

You don't have to stop or block your website from working on Shabbat, though it is a blessed action for the reasons ahead. Even though it's Shabbat by you, a Jew elsewhere, not yet or no more in Shabbat, can access the site. If a Jew enters your web site on Shabbat; strictly speaking, it is his problem and sin but not yours as you leave the site open for Jews on their Friday or Sunday. However if a Jew breaks Shabbat and buys from your site during his Shabbat, you enter a Halachic problem of benefiting from a Chilul Shabbat, regardless to the fact you deposit the money later on. You can explicitly ask those who use your website not to perches anything during Shabbat if you can't simply block the option to buy. (See Techumin 19 p.349 – 363, Techumin 20)