You don't encrypt a website with SSL. you encrypt the connection. Therefore if you have SSL enabled for the webserver simply adding https:// to the url will encrypt the connection and whatever page the url points to will be encrypted while in transit.
so https://www.website.com/index.html is encrypted and http://www.website.com/index.html is NOT encrypted
I prefer for that to never happen so I always put my encrypted pages in a subdomain eg. https://secure.website.com/index.html
SSL comes with a couple of gotcha's
1/ a basic SSL certificate will only be valid for a specific domain name so if the certificate for is www.website.com and someone follows a link for website.com a warning will be displayed. (see note below)
2/ SSL requires a dedicated IP (which you appear to have). that means you may have problems if you are on a shared platform. this is because in HTTP the host or domain name is part of the headers but the headers are encrypted so the server can't know where to route the request to. (see note below)
It sounds like you really need to employ the services of someone familiar with ecommerce and SSL to help you. navigating the minefield with limited knowledge and forum responses is not the safest thing to do. especially if financial transactions are taking place because there are other requirements that must be considered such as the legal requirements in storing and using financial information such as credit card numbers.
DC
Addendum:
For donations consider Paypal. They have a complete donation solution and more people will trust it than a roll your own solution.
EDIT 2016: The world moves on and some of the advice above is not as true as it was when originally answered.
SSL no longer requires a dedicated IP address. SNI (Server name indication) resolves that and is almost universal now (IE8 on winXP does not support it and a few phones).
You will find most certificate vendors now include the main domain name as a SAN (subject alternative name) in a certificate. Which is to say they will provide a certificate for both www.website.moc and website.moc if you get a certificate for www.website.moc. Do not assume this, make sure your certification authority specifies it.