Below is an example that worked for me, you have to use an XPath selector in order to inject your rule into the proper position via the xdt:Transform
property.
<?xml version="1.0" encoding="utf-8"?>
<configuration xmlns:xdt="http://schemas.microsoft.com/XML-Document-Transform">
<system.webServer>
<rewrite>
<rules>
<rule name="CanonicalHostNameRule1" enabled="true" stopProcessing="true"
xdt:Transform="InsertBefore(/configuration/system.webServer/rewrite/rules/rule[position() = 1])"
>
<match url="(.*)" />
<conditions>
<add input="{HTTP_HOST}" negate="true" pattern="^www\.yoursite\.com$" />
</conditions>
<action type="Redirect" url="http://www.yoursite.com/{R:1}" />
</rule>
</rules>
</rewrite>
</system.webServer>
</configuration>
You can do some other interesting replacements using xpath statements as well. I hope the above example is helpful as StackOverflow is generally where I look first for this type of thing these days.