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Did you say you are using this SDK sample? http://help.arcgis.com/en/webapi/silverlight/samples/start.htm#WebMapDynamicServicePopups. This SDK sample use an existing map from ArcGISOnline to build a client-side map.
Clearing/adding graphics to map:
If you are working with ArcGISDynamicMapServiceLayer, you can set VisibleLayers to empty int to hide the features: http://help.arcgis.com/en/webapi/silverlight/samples/start.htm#SubLayerList. If you are working with GraphicsLayer/FeatureLayer, you can call layer.Graphics.Clear() or layer.ClearGraphics() to remove features from graphic collection. http://help.arcgis.com/en/webapi/silverlight/help/index.html#/Using_a_Draw_surface/01660000000s000000/, http://help.arcgis.com/en/webapi/silverlight/samples/start.htm#DrawGraphics.
This concept page might help on how you can create your map: http://help.arcgis.com/en/webapi/silverlight/help/index.html#/Creating_a_map/016600000011000000/. If you have your data published as service in ArcGIS server, you can consume this by setting Url property of the layer. If you will be working with SQL directly, you can use WCF service to send/receive geometry: http://blogs.esri.com/esri/arcgis/2010/03/11/sending-geometry-between-silverlight-and-the-server-using-wcf/.