Copy all the XSD files in one directory and upload it in a link which is accessible to your PRPC. Instead of Uploading the XSD document you can use Document URL option and give the link of your main XSD document. This way PEGA will automatically include all the sub XSD's. Hope this helps!
You can refer the child xsd's in parent xsd. No need to copy all the contect of child xsd's to parent xsd. Parent xsd should have reference of child xsd so that at run time of consuming the xsd to PRPC application child xsd's will get pick up.
This is what we did in our project. You may need help from application server team to accomplish this task.
First create a folder in your WAS server and put all the XSD files in that folder. Then expose them as a directory link using a command and give full permissions to that directory so that PEGA can able to access the link. Sample as follows,
Create a folder names test1 under WAS directory and copy the files /appl/inv/acpt/was/test1
Then create a link using this command Alias /test1 /appl/inv/acpt/was/test1