Generally, planting each stem individually is best, but in small bunches should be fine for most stems. If your substrate is deep enough, just take the base of them stem in forceps and shove it as deep into the gravel as you can.
And just so you know, it's normal for stems to grow roots above the substrate. They just help anchor the plant in place. If you don't like the look of them you can clip them off, but there's no harm in leaving them.
And just so you know, it's normal for stems to grow roots above the substrate. They just help anchor the plant in place. If you don't like the look of them you can clip them off, but there's no harm in leaving them.