When you use batteries together like that they SHOULD be very similar batteries. Doesn't matter how you connect them because the weakest batteries will charge first and tell the charging system they are charged thus never fully charging the stronger batteries. NEVER mix a deep cycle battery and a standard battery. They MUST match in type and approximate age or you will have issues or a shorter life span than normal for one of the batteries.
Series batteries provide double the voltage... But if you are using 2 batteries of different capacity or age where they are measurably degraded you will never fully charge the good batteries thus reducing their life dramatically.
If you do them in parallel they generally double the storage capacity. But again the batteries need to be similar in type, size and age.
If you decide to use a deep cell battery and a standard battery you must use a digital style charging system or you will reduce the life of one of the two batteries. Which one will depend on their characteristics. Other option is a separate alternator for the deep cell battery.