There is only one charger entering the motor at any time the manifold, now some people route their plumbing a little differently.. Follow, air enters atmosphere charger, compressed now can either go to the intake side of the manifold charger or dump directly into the intercooler reversing the flow that it has now, then to the manifold charger then directly to the motor.. Now going to the compressor inlet on the manifold works just like what you have routed in with the current charger, either you cool one stage or cool two its your choice.
What i look at it is usually if any one given turbo is gonna let go it will most likely be the manifold turbo because of back pressure issues 99% of the time. Hence why most intercool both stages to save their motor from being trashed in the event of a catastrophic failure, but if for some reason your atmosphere lets go you trash both turbos.
I don't know about where you are at but complete 7.3's can be had for a lot less than replacing two turbochargers hence why i will only cool the atmosphere.
And in response to the 38r or 40r it doesn't really matter which the flow in lbs/min is not what you are after, you could literally take a 35mm inducer turbo as your high pressure as long as it had a huge exhaust side to move the drive away from itself, or a monster ass gate. The 40r is a little stouter turbo bigger all around on the exhaust, compressor, shaft.. Its your pick i just happened to be able to pick up a 40r for 1200 brand new that's why i went that route...
And yes i will be more than happy to post up pics of it all going together and exactly how i did everything for anyone that wants to know.. When i get that far LOL