In order to configure a new store on top of a folder containing an image collection, you simply needs to navigate to the GeoServer's gui "add store" page and then select the ImageCollection raster data source. Then, select the folder you want to use as root of your image Collection and continue configuring the store as a standard raster store.
Specifying WMS requests.
Once you have configured your coverage, you can start sending WMS GetMap requests to access an image available on the collection.
In order to send a getMap request to access the E.TIF image contained on myCollection/folder2/subfolderB you simply need to append a CQL_FILTER to the getMap request, like this:
Make sure to always specify a
CQL_FILTER=PATH='pathToRequestedImage' since geoserver actually has no way to send a default path to the request (This will require some hardcoding).
Finally, if your image is 1000x1000 pixels and you want to get the area of the image contained within a rectangle (x0,y0 x1,y1) (As an instance, x0=400,y0=400 x1=700,y1=700), make sure sur to specify a BBOX parameter where Yi are specified with negative coordinates. As instance, for the same example, you need to specify
BBOX=400,-700,700,-400. Make sure to respect minX,minY,maxX,maxY syntax.
Moreover, the width and heigh height getMap parameters allow to force the requested image area to fit into the specified size.