Open MMC, and add multiple Remote desktop snap-ins as you want, then save it to a .msc file
To rename the remote desktop tree, look for the below pattern:
<StringTables>
<IdentifierPool AbsoluteMin="1" AbsoluteMax="65535" NextAvailable="10"/>
<StringTable>
<GUID>{71E5B33E-1064-11D2-808F-0000F875A9CE}</GUID>
<Strings>
<String ID="1" Refs="1">Favorites</String>
<String ID="2" Refs="4">AD</String>
<String ID="4" Refs="5">Exchange</String>
<String ID="5" Refs="5">Virtuals</String>
<String ID="6" Refs="5">Managment</String>
<String ID="3" Refs="2">ADIB</String>
<String ID="7" Refs="5">SQL</String>
<String ID="8" Refs="5">CITRIX</String>
<String ID="9" Refs="1">Temp</String>
</Strings>
</StringTable>
below is the block that represent a single remote desktop snap in, to knows its display name, match the numbers in <String Name="Name" ID="X"/> below
and <String ID="9" Refs="1">Temp</String> above.
<Node ID="98" ImageIdx="0" CLSID="{3D5D035E-7721-4B83-A645-6C07A3D403B7}" Preload="false">
<Nodes/>
<String Name="Name" ID="9"/>
<Bitmaps>
<BinaryData Name="Small" BinaryRefIndex="28"/>
<BinaryData Name="Large" BinaryRefIndex="29"/>
</Bitmaps>
<ComponentDatas>
<ComponentData>
<GUID Name="Snapin">{3D5D035E-7721-4B83-A645-6C07A3D403B7}</GUID>
<Stream BinaryRefIndex="30"/>
</ComponentData>
</ComponentDatas>
<Components>
<Component ViewID="1">
<GUID Name="Snapin">{3D5D035E-7721-4B83-A645-6C07A3D403B7}</GUID>
<Stream BinaryRefIndex="31"/>
</Component>
</Components>
</Node>
The above block is helpfull also when you want to re-arrange snap-ins.