When you have a full backup and a set of log file backups, a log chain is maintained using the LSN (Log Sequence Number). If you want to do a backup without breaking the log chain, then do a copy-only backup.
If you do not do a copy-only backup, the log chain is broken and the backup you take will be the latest full backup. This means that the previous log backups cannot be applied to the newly taken full backups. The log chain is mostly maintained for point in time recoveries or log shipping scenarios.
For example: say you have a backup scenario that takes full backups every 6 hours (midnight, 6 am, noon, 6 pm) and log backups every 15 minutes. A request comes in at 9 am to have a copy of your DB placed on a test server. You want to take the backup without breaking your log chain or disrupting your backup jobs. This is when a copy-only backup is taken. The copy only backup will not disrupt your regular backup sets.