Question

How I can to change the values X, Y of a node?

Answer 1

Click on the node, then either drag it to the desired new coordinates or explicitly enter the desired coordinates in the properties view in yEd's lower right corner.

Answer 2

There are several ways to change the X and Y values of a node.

1. Select the node and move it with the mouse.
2. Select the node and change the values of X and Y in the Properties View.
3. Select the node, press F6, and change X and Y in the Properties Dialog.

Or are you trying to do something more complicated, like automatically assigning coordinates to nodes?

Comments

My target: X, Y coordinates in Excel => coordinates in yEd

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For this, add additional columns for X, Y coordinates to your Excel spreadsheet, import those as custom properties (the columns with their values need to be part of your 'node list'), and don't do an automatic layout as part of the import.
After the import, use the Properties Mapper dialog (http://yed.yworks.com/support/manual/properties_mapper.html) to directly map the values of your custom properties to the X,Y coordinates of each node.