Where should I store my aspx file and web.config if ....

I am using a webhost and I need to copy my aspx and web.config files to:-
webhost/
It is now working properly. However, I actually has 2 apps and I do not want their aspx file and web.config to mix together in same directory.
Where should I store my aspx file and web.config of these 2 apps ?
Now I create 2 folders, namely: webhost/system1 and webhost/system2
and copy all files and subfolder that are now currently under webhost/ to webhost/system1
Now instead of typing www.[mywebname].com, I goto www.[Mywebname].cm/System1 and press enter
on run, I get this error point to web.config file:-
It is an error to use a section registered as allowDefinition='MachineToApplication' beyond application le ...