Rather depends...
As Vern's are hand made to order, they come in various sizes. As far as I know (but check directly with Vern), he made two widths and two lid heights. Best check directly with THE MAN himself however.
I have a pair of the narrower ones (minus 2" width), with standard height lids (tall lids would have looked odd). I found a pair of relatively cheap roll-up Samsonite travel bags that fit well, allowing a bit of room in the angled bottom for tools etc. and a bit of space in the lid for odds and ends. Work perfectly.
If you have the 'standard' width jobbies, I'd suggest you measure the boxes and include that in your post. Might allow people to compare with other makes and give you alternatives.
Whichever way - if you use any kind of plastic/nylon bag, I hope you have the heat/silencer problem on the left box sorted - I've got T-shirts with plastic melted onto them, a melted number plate and a couple of melted L/H rear indicators so far.
Vern's an outstanding craftsman and good chap, so if you haven't got the heatshield sorted, I'm sure he'll help you out. I've found that the exhaust extension tube makes the biggest difference. Having said that, I have the silencer-side face of the left box covered with a heat resistant board I managed to find. Inside is now cool as a cucumber...