The best ways to valour up spies/assassins are:

1) Train pre-valoured up agents using the improved brothels and taverns available in MTW/VI 2.01.

2) Put them on the defensive counterspying in your provinces. If you plan to do this then you should not build border forts as this will make your spies/assassins redundent.*

3) Send them on easy missions within your own provinces or rival provinces without border forts. Try to keep track of them so that they don't go wandering off... to their deaths.

*My preferred method.