Yes, always keep the female separate, it’s a confined space and stressful enough.
If you have a female bearded dragon attempting to lay eggs and you keep her in the company of other dragons, ideally you will need to remove her or her companions to their own vivarium.
Having seen dragons lay eggs in a community within large tanks, it’s more a question of wellbeing, the best results have always been achieved in isolation, unless the communal tank has a floor area larger than 16 square foot it seems to be more stressful on the individual – Especially if the male is kept in that same environment.
Captivity in any enclosed environment can be stressful enough, even with a tank as big as 16 cubic feet. I find in general a floor area of 8 square foot is only just passable for the larger beardies, both for space and maintaining an adequate heat gradient. Even without them developing eggs, I found the dragons kept together suffered as there would be dominant behavior, such as nipping and stealing food.
Consider egg binding, this is where the female beardie is unable to lay her eggs, which sometimes can be caused by lack of fluid, calcium, energy but also stress from not finding a suitable burrow or perhaps being hassled by her co-inhabitants.
The female beardie is looking for somewhere to dig and needs at least 4 inches (10cm) of soil/ sand substrate to dig in and lay her eggs – that substrate also needs to be kept damp to maintain form and the more of it the better. She’ll spend a long time digging and re-digging a burrow before laying, the last thing she needs is unwanted attention.
Laying eggs is also very tiring for the dragon, she needs a good source of nourishment and will have a voracious appetite due to the energy that she’ll expend both in burrowing and laying. We can always tell when ours are due to lay eggs going by appetite and their size.
You’ll need a suitably sized tank for laying eggs, the best bet is to permanently house the bearded dragons separately because the agamid lizard-like most others will lay multiple clutches of eggs over a period of time, if fertile, I’ve seen this to be 6 clutches, 1 clutch every 2-3 weeks. Infertile, this seems to be less frequent, normally once every 4-5 weeks and sometimes only the one clutch.
I’ve seen some beardies lay eggs in a small container of soil and hop out again, I tried this method for my own as it’s far cheaper than buying a separate tank but I had little success in them laying the eggs – my lot may be a bit fussier.
Unlike me, if you’re in a warmer climate, then there’s nothing stopping you from creating a temporary pen outside in the sun to give them as much space as they need to dig down and burrow. You can get or build a pen for relatively cheap, just remember to keep a mesh over the roof and a floor that will stop them digging through and escaping.
If you intend the breed the dragons then you’ll want to remove the eggs which you can read more here about caring for the bearded dragon eggs otherwise you can leave the eggs in the substrate – I’ve yet to see any eggs survive or hatch, they normally shrivel or get dug up again by the female.