-Clearing junk depends on the memory limitations of the device.If you have more memory(4Gb or more then you can avoid it but at some point of time you have to clean) then you don't need to clear the junk files as the device will simply store it on board.But if the device's on board memory is less <=2Gb then you have to clear the junk files quite often.(In case you have 15-30 apps installed then your phone may start responding late/worst case stuck)
-Junk cleaner applications usually clean the cache memory/files >10 Mb as well as the files which are left after uninstalling an application.
So in order to them manually you can follow these steps
-For simple tasks like clearing images/videos you can delete it from the gallery directly as the gallery sorts them based on the app.
-For cache you need to clear the cache separately from app menu.
Only for removing un-instaled app data you need the cleaner.
-Ex:-If you use whats app then you can manually delete the videos/pictures shared from the whats app folder by Videos/Images section.But if you directly delete whats app folder then you will lose all the chat data/backup as well.
Note:-If cleaning each and every applications cache is cumbersome then you have to use the cleaner application.Having more on board storage space does not remove the necessity of cleaning it only delays the frequency of cleaning.
Caution:-Do not delete any file blindly from your device.Cross check the file name with the existing list of applications.As deleting files may cause loss of data to that particular application.By time you will be able to identify the file structure