So I am still learning a good bit of course, but I thought I would share my experience.

I was using BIDS to develop SSIS packages and loading them onto the SQL server through that. The problem was that I couldnt then remove the old packages from the server because I was not able to connect to MSDB when connected to IS through SSMS. (I got the: the sql server instance specified in ssis service configuration is not present or is not available ... error). I tried editing the config file to no avail.

I am still not able to get into the MSDB folder, but I found an alternative:

You can use the table [msdb].[dbo].[sysssispackages] while connected to the DB Engine.

to view and then update, delete, or whatever you want to do to the stored packaged.

Just sharing!