If you laid the flags directly on the ground, then I wouldn't bother with mortar. The first freeze-thaw cycle you hit this winter, the mortar will crack and fracture. Just fill in between the flags with soil and plant in spring with a creeping ground cover or use a coarse sand to fill in between and skip the plantings. It will hold up for a few years but eventually the stones are going to raise or become uneven and could crack and the surface will no longer be flat.

If you want a more permanent, mortared surface then you will need to redo this project correctly.......and there is a right way to do it :-) This link will show you how to do a dry install - when done correctly (as the article outlines), it can be as stable and permanent an installation as a mortared one. But a 'wet' or mortared installation is a bit more complicated as a DYI project.

I live just outside of Phoenix AZ and we only get a few light frosts. This year it looks like we aren't going to have a winter, we are hardly getting a fall. It took me quite a long time to do this one and I don't think I could take it up and redo it.

If you get no serious ground freezing, then you will probably be OK. I still wouldn't bother with any mortar - it won't hold up well with this sort of construction and it's a lot of work to do well and with a professional looking result. For a mortared patio you really should redo properly with adequate base layers, etc. But the flags on the ground should be fine if you fill in between with sand or plant the voids with ground covers.

I gets to hot here in the summer for planting between the flagstones. this last summer we hit 117° for several days. Most of my regular plants cooked so anything between the stones wouldn't stand a chance.

I know it is going to be a job putting down the mortar but you only live once so what the heck I might as well try.

It would be better to plant something between the stones. They will settle and the mortar will break without a compacted foundation. Something that is more a particle like a sand will not show the breaks and will resettle. But the stones will hold moisture real well. Emerald moss or miniature lily like mondo would like it if it is even semi shady. You could sweep in a seed mix with the appropriate mix and it will pop up and look beautiful if you have left some spaces.

Yes, type S mortar is the correct mortar. However, please reference @dirtmechanic "There are sand mixes with polymer additives that you sweep onto laid stone and pavers that you simply moisten. They duplicate the mortar effect, but are flat out easier to maintain over time as well." He or she is 100% correct and polymeric sand is readily available. It will be far easier to install and will look identical to mortar.

Another vote for either just sand swept into the spaces or the sand/polymer mix.