This software is designed for "download once - install many (computers)".
If you use it to update a single system, you may of course delete the whole software once you've downloaded and installed the missing Microsoft patches.
Don't delete the repo if you intend to update the system(s) in the future. Otherwise you need to download everything again, then.
Microsoft update catalog: http://catalog.update.microsoft.com/v7/site/ Windows Install media download: https://support.microsoft.com/en-us/help/15088/windows-create-installation-media
Did you download the patches matching your OS and architecture? For 64bit-Systems you need to use the update sets ending in -x64, e. g. w61-x64.
Microsoft update catalog: http://catalog.update.microsoft.com/v7/site/ Windows Install media download: https://support.microsoft.com/en-us/help/15088/windows-create-installation-media