Ah, I seem to have gotten it to work! Just had to restart Fusion, that was all.
I created my own Fusion360.xml files and placed them in
%appdata%\3Dconnexion\3DxWare\Cfg
and
C:\Program Files\3Dconnexion\3DxWare\3DxWinCore64\Cfg
Here's the file that goes in appdata, the other one is attached
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<AppCfg Default="false" xmlns="" CfgFormatVersion="1.0" ThisFileVersion="1.0" xml:space="preserve">
<AppInfo>
<Name>Fusion360</Name>
<ExecutableName>Fusion360.exe</ExecutableName>
<Transport>S80</Transport>
</AppInfo>
<CfgProperties>
<InheritsFrom>Fusion360</InheritsFrom>
</CfgProperties>
<Settings />
<Devices>
<Device>
<Name>SpaceMouse Wireless</Name>
<VendorID>46d</VendorID>
<ProductID>c62e</ProductID>
<AxisFilter>None</AxisFilter>
<Axis>
<Enabled>True</Enabled>
<Input>
<ActionID>HIDMultiAxis_X</ActionID>
<Min>-512</Min>
<Max>511</Max>
</Input>
<Output>
<ActionID>HIDMultiAxis_X</ActionID>
<Reversed>False</Reversed>
</Output>
</Axis>
<Axis>
<Enabled>True</Enabled>
<Input>
<ActionID>HIDMultiAxis_Y</ActionID>
<Min>-512</Min>
<Max>511</Max>
</Input>
<Output>
<ActionID>HIDMultiAxis_Z</ActionID>
<Reversed>False</Reversed>
</Output>
</Axis>
<Axis>
<Enabled>True</Enabled>
<Input>
<ActionID>HIDMultiAxis_Z</ActionID>
<Min>-512</Min>
<Max>511</Max>
</Input>
<Output>
<ActionID>HIDMultiAxis_Y</ActionID>
<Reversed>True</Reversed>
</Output>
</Axis>
</Device>
</Devices>
</AppCfg> It doesn't seem to save settings, I'll see if there's anything I can do about that.