I do use FileZilla, but that's not the issue. Apparently it's a structural issue with how Joomla 1.0 works with PHP and Apache and cannot be avoided. When you import a template from within Joomla the "owner" is automatically set to the System level account. The files become "owned" by a HostPapa account which you have no control over. Support will change the owner for you, to "your" account, but what a pain... I did find several solutions....
Joomla 1.5 wasn't even released last month when I had this issue and Fantastico is still showing v1.0.14. But the newest release of Joomla imports templates etc. using your FTP account so it avoids this whole issue.
First and foremost, J! 1.5 will solve much of these permission problems with it's FTP installer. Since the website will operate using your FTP account instead of the default Apache account of nobody or WWW, there will be no more issues between what the server needs to work and write status using your FTP client. Basically FTP account will remain the owner of all files and Joomla will write any files it needs to write using the FTP account.
Some hosts offer this solution but the Sysadmin confirmed HostPapa does not have SUEXEC.
suexec is a system by which apache Switches User and EXECutes the process based upon the user that owns the document root for the particular virtual host being requested. (catch the SUEXEC in that?) This is a solution that some hosts offer, and allows for all files created/modified/etc... by the apache processes to be owned by the proper user.
This was another alternative and the Sysadmin who was helping me did set up a CRON job for me that does this and it has been working great! I have not had any problems since.
My hosting company created a cronjob for my server which sets "chwon -r" to all my sites files to the same user every 5 minutes.
So when I install a component via Joomla, the owner is Apache and the files cannot be deleted/modified using ftp.
But 5 minutes later the owner is the same as for all other files, and I am free to delete/change it using FTP.