You can get a specific Layer by assigning layer identifier to LAYERNAME property.
Something like the following:
private ILayer GetSpecificWMTSLayer(string url, string layerID)
{
IWMTSLayer wmtsLayer = new WMTSLayer();
WMTSConnectionName connectionName = new WMTSConnectionNameClass();
IPropertySet propSet = new PropertySetClass();
propSet.SetProperty("URL", url);
propSet.SetProperty("LAYERNAME", layerID);
connectionName.ConnectionProperties = propSet;
wmtsLayer.Connect(connectionName as IName);
return wmtsLayer as ILayer;
}
These are the seven properties you can handle with your property set:
URL, LAYERNAME, USER, HIDEUSERPROPERTY, VERSION, PASSWORD, CONNECTIONPATH