Question : Any good insights to Web Deployment  from Visual studio 2008?

I have a web application which has become quite large and will soon be moving it to online
host. I know there will be bugs to be worked out. Is  there a good way to do this considering the
following:
-  uploading the complete site can take a long time.
-  I do not want to leave source code on the web server.
I read that if I compile without allowing for updating  then even if make small changes I must
recompile and upload the whole site but If I allow for updating then my source is exposed on
the web server. Is this correct.?
Must I shut down the web application while an update is uploading? If so, how do you get users
to close their sessions so an upload can be done? Is there a way to have minimal down time
while make changes?
Any thoughts on deploying would be appreciated.  I've used visual studio 2008 with visual basic
and heavy use of master pages. There is a SQL 2005 DB which has hundreds of stored procedures.
Thanks

Answer : Any good insights to Web Deployment  from Visual studio 2008?

If you have a time stamp for one of the connection refuse errors, I would look in the system and application event logs to see if there is a corresponding event around that same timeframe that my indicate the reason for the refusal.   Of course, if it is not actually causing any issues, I may be tempted to chalk it up to normal operations.