Well, it's a full mortar bed you need, then. Something along the lines of an 8:1 or 10:1 mix of grit sand and cement, with little or no added water, so that it's what we call a semi-dry mix, for the bedding, and a Class II mortar (4:1, roughly) for the jointing.
It's a good idea to work out a laying plan in advance, so that you start in the far corner, and work your way out. If you know the sizes of the flags you'll be laying, it's easy enough to work out a plan similar to those shown on the
Random Layouts page which will save a lot of head scratching and frustration when you're doing the actual laying.
Use a starightedge, at least 2.4m in length, to keep checking the floor for level. Unlike an external patio or pavement, there's no need for any fall, but, with stone flags, it's very easy to be misled, and what you think is 'level' is anything but. Trust your laying lines, the straightedge and the spirit level, rather than your eyes and intuition.
Have you thought about using a sealant once it's all laid?