Go into the help menu...Proteus VSM help...my copy sounds like yours, they work yet they don't really work, I have to go through it page by page to find what I want...you'll eventually find an interactive simulation tutorial that will guide you step by step to simulate a circuit. It will include attaching the source file and allow you to further read Source Code Control System. You'll get lost if someone tries to tell you each step here....best to use the built in tutorial. I don't know what a .s19 file is but you'll find out what types of source files are supported in the tutorial links.
There are other topics covered including code generation tools and debugging when things don't go right. Not sure why your help files aren't working properly, maybe uninstall and reinstall program.
The problem with your pins...usually gnd, vcc, etc....they are probably hidden, not shown on the chip....but if you put your mouse over the chip and click the right button then the left(I know that sounds like a weird combo) an edit component window will pop up...to the right you'll see a button called hidden pins, click it, whatever the pin says the net should be the same, unless you know what you're doing and want to customize it, but this requires you to setup the same in another area, which is the next step...go to the menu Design and find Configure Power Rails...Power Rail Configuration window will pop up...the name should also match the nets connected to, just like whatever is in the hidden pins window....this may be hard to follow but you'll get the gist of it.
Hope this helps.