Вы можете использовать bwlo URL rewrite rule:
<rule name="rule1" enabled="true" stopProcessing="true">
<match url="(.*)" />
<conditions>
<add input="{HTTP_HOST}" pattern="^app1.domain.com$" />
</conditions>
<action type="Redirect" url="http://localhost:80" />
</rule>
<rule name="rule2" stopProcessing="true">
<match url="(.*)" />
<conditions>
<add input="{HTTP_HOST}" pattern="^app2.domain.com$" />
</conditions>
<action type="Redirect" url="http://localhost:90" />
</rule>