I finally have a good option to import data from different sources. Yes the Microsoft Dynamics CRM 4.0 comes with a good tool to import data with lot of features (mapping, duplicate detection) but when you would like to import data and after update it you have to export it and report it.
Our development team prepared a good add on for Microsoft SQL Integration service, which is capable to import and update records on selected unique key
You can set the parameters for the CRM server (we currently use 2006 web services)
And you decide in which entity you will import the data from the selected source.
You get the source columns and you can name them with the appropriate names in CRM (mapping)
For the selected columns you can set the compare key for the selected attribute.
So we have the right tool to import and update the records on schedule from different applications.
Well done Matej..