Cake flowers are one way to make something simple really pop. Unless you're having a really complex styled cake or sugar flowers, consider asking for a florist for a few stems of flowers or greenery for your cake. Especially if you have a simple or plain cake, it doesn't take a lot to make it look more personal.
Typically both the florist and the cake artist know how to incorporate flowers into the cake and who puts them on will depend on the timeline. If the florist is still setting up when the cake is delivered, they will be happy to place the flowers, if the cake is delivered after the florist has already left, they will usually leave the stems for the cake person to place. For this reason, if you have a specific vision of where you want the flowers placed, be sure to send the picture to both the florist and the cake artist. It's also helpful if you let them both know the other's name, contact information, and timeline so they can plan around each other.
If you are using real flowers on your cake I would not recommend eating them or the section of cake they are on. Unlike produce, a florist does not have the option to wash the flowers before sticking them in (yes the stems get poked into) the cake. A florist can but doesn't always wrap the stems in floral tape to keep the stem from getting on the cake, but the rest of the flower will likely be touching the section of cake it is in. Florists often don't have the option to order organic flowers and since it's unsure of their growing conditions, it's best not to eat the parts of cake the flowers are in, and definitely don't eat the flowers themselves.
You can also do flowers underneath the cake to make a statement without actually having flowers in the cake, or in between layers of the cake. Some cake artists will have fun stand options that can be decorated and be really showy.