What type of media are they set as in iTunes? If they are set as "music", and if you have iCloud Music Library on, then they will be treated as music and will sync automatically to all your devices your iCloud Music Library is active on, assuming they satisfy the conditions for being in your iCloud Music Library (maximum length, file size, bitrate etc.). In that case, they will count towards the 100,000 song limit of your iCloud Music Library, not towards your iCloud storage plan.
Not sure what you mean by safe. As long as you're subscribed, to Apple Music/iTunes Match, the content of your iCloud Music Library will remain in the cloud untouched; only if you unsubscribe, you'll have to download them from there in-time. (Though offline-backups are always a good idea...)