Well, if you consider a Dedicated server for your E-commerce sites, you will have several advantages and the best one will be the availability of your E-commerce sites which is really important. If you consider a Dedicated server for your sites, your E-commerce sites will be available all the time as 100% uptime guarantee is offered with Dedicated servers (atleast, BODhost offers ;)).
When it comes to handling a Dedicated server, it is not difficult if you consider a fully managed Dedicated server
Yes, changes in the setup of your sites and other applications is to be done but this is not a difficult task if you consider a fully managed Dedicated server. Also, if you consider a Dedicated server, considering it with a control panel will be a good option as this allows you to manage your server quite well
