do I put all the www of each app together?
No as AB pointed out you create a different folder for each app:
/root/myapp1/myapp1.jar ON PORT 51042
/root/myapp1/copymewithjar.need
/root/myapp1/www
/root/myapp2/myapp2.jar ON PORT 51043
/root/myapp2/copymewithjar.need
/root/myapp2/www
/root/myapp3/myapp3.jar ON PORT 51044
/root/myapp3/copymewithjar.need
/root/myapp3/www
All apps act as different apps. You don't need to have only one www folder for all the apps.