To my knowledge if you put something in the PCIe 1x slots everything should be fine. You run into an issue when the other PCIe 16x slot is used. I suggest reading the manual more to find out.
This means (AFAIK) that as long as you use the PCIe 1x slots your PCIe 16x slot will stay at 3.0 speeds. You only run into issues when you put something in the other 16xslot. The manual will confirm.