on Visual Studio you can publish only one website at a time otherwise there is a clash between one website with multiple website.if you want to do that means on startup of one website other website also publish . for that you need to do some setting on Solutional Level.
follow the steps :
1- on proejct Solution just right click it & select Product Dependencies.
2- select Dependencies tab.
3- select your main website(startup one) from Dropdown.
4- now check all the web service on "Depends on" section
that you can decide how many site you want to publish at a time of this main site.
5- click ok
now whenever you publish that main site , then it will prompt publish window for all other depended site ,then all other mention site will also get publish , if you dont want to publish that you do the same above procedure to deactivated that ,