In early Mac Pros, the system will automatically evenly distribute the number of available lanes to expansion cards. It also means that you may need to reorganize your cards to get an optimal number of lanes assigned to the card. This means that if you have two x16 cards in your system, you will need to compromise the performance of one card in order to run the other at its optimal speed (for systems before the 2009 models).
For instance, if you have two graphics cards in the first and second slots, you can either run both slots at x8 speeds or run one at x1 speeds and one at x16 speeds.
