How to execute custom action only in install (not uninstall)

Add a condition on the action so it's only triggered during installation, not uninstallation.

Action run only during Install

NOT Installed AND NOT PATCH

Action runs during Install and repair

NOT REMOVE

Run on initial installation only:

NOT Installed

Run on initial install or when repair is selected.

NOT Installed OR MaintenanceMode="Modify"

To only run an action during uninstall use the following condition:

REMOVE~="ALL"

To only run an action during upgrade:

Installed AND NOT REMOVE

An example:

<InstallExecuteSequence>
..
    <Custom Action="QtExecIdOfCA" Before="InstallFinalize">NOT Installed</Custom>
..
</InstallExecuteSequence>

..
..
<CustomAction Id="QtExecIdOfCA" BinaryKey="WixCA" DllEntry="CAQuietExec" Execute="deferred" Return="ignore" Impersonate="no"/>

Notice! Condition is added to the <Custom> tag and not the <CustomAction> it confused me, because Custom is followed by Action attribue

A bit of a correction:

Finally, to only run an action during uninstall use the following condition: REMOVE="ALL"

This seems more appropriate as the property REMOVE contains the features being uninstalled.
So if I do a modify to remove one feature, REMOVE is true and the action that was to execute only on uninstall executes on modify.
More details here on MSDN

Please be careful with REMOVE=ALL. It is not available before installvalidate sequence.
And check below links for more details:
http://msdn.microsoft.com/en-us/library/aa371194(v=vs.85).aspx
http://msdn.microsoft.com/en-us/library/aa368013(v=vs.85).aspx

A condition on the custom action, probably with a matching custom action to do the uninstall. Not sure what tools you're using, but assuming the secondary install is tied to a component, I would use that component state. A state of =3 means a target state of installed. A state = 2 means a target state of absent. Note that the state won't be set if there is no change.