Hi Paolo,
I think you should re-read my previous post as it appears you have missed the point I was trying to make. As I said before, you can use your schematic design and the IDAC current source routing as you have it. However, there is no input filtering. Adding input filtering will cause an error when using the IDAC routing as you have it in your design. Also, 2-wire RTDs will have an error as you add the lead resistance to the measurement. It may be a small error as compared to PT100, but it will be a factor when measuring as the lead resistance will add to the PT1000 itself. Adding any additional resistance will also add to the error. You can design your system without input filters, but I can tell you that you will not be happy with the results. The design goal should be to limit the error and control the noise so that it is at a minimum.
If you wish to add input filters to reduce noise, and if you want to minimize the error that would be created by current flowing through the input resistor, then you must source the current independent to the analog input being measured. Your schematic configuration only has two available sources to do this. I recommended changing your schematic to minimize noise and error.
So to answer this last question, yes you can source the IDAC current through the IOUT1, IOUT2, or out any of the AIN0 through AIN7 pins.
The above example only shows differential caps, but common mode filtering caps could also be added.
Best regards,
Bob B