First, make sure you understand that the Aggregate add-in will work only with polygon map layers...not with point or line map layers (if you are unsure about what these different types of map layers are, please refer to the AWhere help documentation, and look for information on 'Map Layer Types'...or you may also refer to the 'Beginner 1' training module, installed with AWhere). So, if it is a point map layer or a line map layer that you are using, then no, you won't see it listed in the Aggregate Add-In, and that is by design.
BUT, if it is, in fact, a polygon map layer that you are using for this Aggregation, then read below for the probable solution.
It is a known issue that a map layer that has a data connection will not appear as a selectable layer in the ‘Aggregate Add-In’ (in ‘Step 1’ of the add-in where you select the map layer to be aggregated). That is, if you have a data connection on a given polygon map layer, and you want to use one of the connected attributes 
(one of the attributes that is being accessed via the data connection) as the attribute on which to aggregate the layer, you can’t do that ‘directly’…but, there is a work around you can use (see below). Normally, when using a polygon map layer that does not have a data connection, you would simply need to display that map layer in the map window, and then when you start the Aggregate Add-In, you would select that map layer as the ‘Aggregate Map Layer’ in Step 1 of the add-in, but in the case of a data connection, the map layer is not shown as being available for selection for some reason.
Here is the work-around solution...you are going to make a copy of the map layer and use the copy for the aggregation.
1. Use your mouse to right-click on the data connection (
)
2. Select ‘Copy’ from the context menu that appears.
3. Choose a folder in the AWhere treeview into which you want to put the copy of the map layer…it could be the same folder that the original map layer is in. Right-click on the folder, and select ‘Paste’ from the context menu that appears.
4. You will now see a new map layer listed in that folder, the name of the new map layer will be a combination of the original map layer’s name, followed by the ‘name’ of the data connection, separated by a colon (i.e. Map Layer Name : Data Connection )
5. Expand that new map layer, and you will see its ‘native’ attributes listed below it 
(that is, attributes that are an actual part of the map layer...not attributes connected via a data connection, which would be identified by this icon -). You will see that not only does it now include the original attributes that the map layer had all along, but it also includes those attributes that had come across via the data connection. Those were ‘connected attributes’, but now they are part of the map layer. So, now that they are part of the map layer (rather than connected attribute), you can use any of them as the aggregate attribute in the Aggregate Add-In.
6. Display any of the attributes from this new map layer, and with the map layer displayed in the map window, start the Aggregate Add-in from the 'Add-Ins' menu.
7. In ‘Step 1’ of the add-in, you should now see this map layer (the copy that you made) listed for selection, and thus you will also be able to now select any one of those attributes to use as the ‘Aggregate Attribute’ for use in the aggregation process.
Also, if you are reading this post and are unsure about what this tool does, read this forum post for an illustration of a scenario of how the Aggregator tool might be used...to create custom territories or regions.