I am in a similar boat, converting an old IS script project to Wix/msi.  So I
am also learning, and very impressed with WIX.  Most of my time so far has
been trying to sort out oddball configuration issues for drivers.  In my
case in some scenarios I need to get printer drivers installed as
print-to-file and in other situations the same driver as pnp when hardware
is attached.  But since the pc is embedded into the hardware the hardware is
attached even before the software is installed, which creates pnp issues.

Given your info, I think I would:
1) create separate msi (without concern about the UI) for each driver.  For
me that means a single MSI project for each of three drivers, each of which
is built twice to create six x86 and x64 packages.  

In the mba try to detect devices or collect registration info and other
configuration in OnDetect.  I do not write anything at this stage.  But the
mba writes info that will be passed to the msi packages as Burn string
variables.  (The bootstrapper project defines these string variables as
bal:Overwritable.  I do not persist these variables since I implement
'remember property' pattern in each MSI.         If you can be certain that
the MSI will not be launched separate from the bootstrapper, then persisting
the variable might be simpler.)

Then in the chain it worked best for me to install the drivers first, (based
on InstallConditions using variable set by the mba) and then install the
application.  In each MSI I implemented 'remember property' pattern for info
that needs to be passed in.  So the info collected by the mba is passed to
each MSI as a MsiProperty.

I'm still learning, so I am interested in other's advice. 





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