I have installed Younity on my computer and have log on to my device with same credentials.
What i have observed is, i am able to see only files which comes under Local Drive C. All stuff other than this is neither available, nor cab be searched.
As i have read in forum, there is no such requirement of keeping the files at a desired location.
By default younity will scan your entire computer, so if you have a lot of files on your computer this can take some time. When you mention " All stuff other than this is neither available, nor can be searched" where are these files located? younity does support external devices via USB if you want to add those as well.
Within younity you have the ability to dictate what you want younity to scan and make available on your mobile devices. To change the default location set to scan- by going to younity / Preferences / Locations and remove your entire home directory and add the locations you want younity to scan.