What you should do is just setup 2 FTP profiles and each would contain the different sub-domain folder. Then in VSD, under the Choose a Publishing Destination, select the correct FTP profile for that website.

That is how they are set up. Each site has it's own FTP profile directing it to it's own URL domain (server info), however again both have the same user name and password to access the server. I have deleted both profiles and re-entered all the FTP profile info for each with the same result.
This worked before without any problems. I can upload the church site fine, but when I upload the school site it uploads to the church site folder (stbonifacecincinnati.com) even though the FTP server info directs it to stbonifaceschool.net

The ONLY way that can happen is if both sites share the same remote folder. You simply need to define the proper remote folder under the FTP Account setup for each website.

OK, I finally figured this out, and I feel stupid.

I found that there are different FTP log ins for the sites even though they are both hosted on the same server. After getting into the server settings I found the FTP info for the school site, entered it to the FTP Settings on VSD, and I'm back in business.

Thanks for everyone's help! And again, this did make me create a list of ALL the log in info for all my VSD sites, the server info, user names and passwords, and the upload folder. If you run several sites I highly suggest you back that info up!

I did this

"Try this.

1. Close VSD
2. Go to Start > Run and type regedit and hit enter.
3. Navigate to HKEY_CURRENT_USER\Software\CoffeeCup Software\ and delete the Visual Site Designer folder.
4. Reboot
5. Now try to add your FTP account again."

And I get the same result. It connects and then the program crashes. I have windows 7 and installed coffeecup into a new computer. My host is godaddy and did new password for the ftp users there as I read in other help answers. The program worked fine in Vista. This is really becoming a pain. Been at it almost 2 hours now.

What is going on? Why connect and then crash?

Please open a support ticket for this and one of our techs will help you out.

This is what happens every time it connects. I have allowed Coffeecup in my antivirus and firwall settings as well.

This is what happens every time it connects. I have allowed Coffeecup in my antivirus and firewall settings as well.

Try this.
Configure the shortcut to always run as administrator. Here's how:

1. Right-click the shortcut icon, and click Properties.
2. Click the Compatibility tab.
3. Here, put a check mark by Run This Program as an Administrator.
4. Next, put a check mark next to Run This Program in Compatibility Mode For: and ensure Windows XP Pro Service Pack 2 is selected.
5. Click OK.