The "structure" of the document (the hierarchy of the tags '<xyz>...</xyz>' is not good.
Here is how it should be:
<SimBase.Document Type="Launch"version="1,0">
<Descr>Launch</Descr>
<Filename>EXE.XML</Filename>
<Disabled>False</Disabled>
<Launch.ManualLoad>False</Launch.ManualLoad>
<Launch.Addon>
<Disabled>False</Disabled>
<ManualLoad>False</ManualLoad>
<Name>AICarriers</Name>
<Path>C:\Program Files (x86)\AICarriers\aicarriers.exe</Path>
<CommandLine>-nogui</CommandLine>
</Launch.Addon>
<Launch.Addon>
<Disabled>False</Disabled>
<ManualLoad>False</ManualLoad>
<Name>Aerotow</Name>
<Path>Aerotow\Aerotow.exe</Path>
<CommandLine></CommandLine>
<NewConsole>True</NewConsole>
</Launch.Addon>
</SimBase.Document>
The problem was that in your version, the "SimBase.Document" was duplicated.
With the structure above, it should work correctly and you should get the popup asking if you want to allow Aerotow to run when you launch FSX.
Please note that your Aerotow folder should be located in your main FSX folder. So for example, if your FSX is installed in d:\FSX\, then your aerotow.exe file should be in d:\FSX\Aerotow\
From what you wrote above, you have done this move correctly already
