I've been working on this myself for quite a while
ftp local is simple enough: firefox or IE will work:
ftp://admin:password@yourdomain.comRemotely I've had some trouble but essentially the same
For IE you may need to set the internet options section/advanced tab/scroll down to and select passive mode for ftp sites
And login to your primary as described above and navigate to your ibay/Primary folder you should see your cgi-bin,files,html etc.
Firefox will not remove or add folders to my knowledge via ftp, however IE should work fine and you can set permission on your folders via right click to properties etc.
As far as disabling the start page link, I"m assuming your talking about in the server-manager etc.
Good question, are you planning on letting others login to the SME other then you, I"M guessing yes to that as well
I wish I could be more help on that topic, sounds like someone will have to give you console directions on that one.
Assuming there is nothing in the documentation on this topic
I hope this helps