You do not specify, but I assume that you refer to stains like propidium iodide: you have to test the usualy range of concentrations and time for staining (i.e. removal from staining solution and washing) for your own setting, which is e.g. also influenced by the growth conditions of the plants. Thus, you will find a good compromise for your imaging.

Vacuum inilftration may not be so helpful, since Arabidopsis roots do not have air spaces which are to be filled by that procedure.

Using a confocal microscope, you may also test other functions like reflection or self-fluorescence of cell walls.

Good luck!

I am using an SR2200 stain for 2 hours and 0.2% concentration, 5-6 days old young Arabidopsis roots. I washed the roots post staining for 4 days. The epidermis, endodermis, and cortex layers are stained well but the vascular layers are not