How do pilots make rudder inputs during negative G flight?
The short answer is that at negative 2 G, the airframe limit for the A7-E, it took little effort to keep your feet on the rudder pedals.

In controlled flight there are aircraft limitations on both positive and negative G. I flew the A7-E for the US Navy and have some operational experience that might offer some context to the question.

I believe the positive G was limited to somewhere between 7-9 G. Can't quite remember the exact number, and it did depend on the external store configuration as well. Newer aircraft have higher G loading capabilities, although the human body has its own limit. Fitness and training can extend the pilots envelope to high G. 

As mentioned negative G in the A7-E was limited to -2. There was no issue at these sorts of values keeping your feet on the rudder pedals. It is worth mentioning that the rudder is controlled by the AFCS (Automatic Flight Control System) system and so there is no real need to keep your feet on the pedals, although I did use them at times. Negative 2 G's was hard on the body, and a pilot would come back to the ship with bloodshot eyes after undergoing maneuvers that required this sort of thing.

I can think of 3 times that a pilot would find themselves in a negative G environment. I am not including standard acrobatic maneuvers, but more tactical situations. One, and this wasn't typical, was during training. At a high altitude you unloaded the aircraft to -2 G's and set a 45 degree dive. As the airspeed increased it entered an area on the IAS instrument that was no longer valid, and this was close to Mach. The goal was to observe the characteristics of the aircraft when it went supersonic. There was a gentle pitch down as you broke the sound barrier. I did this maneuver once, although I commonly practiced 45 degree dive bombing deliveries.

The second, and quite common, situation was a maneuver called a bug out. A bug out was used by a flight to engage other aircraft in air-to-air combat. It was at once a defensive and offensive maneuver. The lead called "Bug out. Bug out," and the flight went to -2 G's, unloading the aircraft, and giving up altitude for airspeed. As your adversary turned towards your 6-o'clock the flight would "Pitch back," and pulling positive G's, gaining altitude. Trading airspeed for altitude got the aircraft into slower flight where its turn rate could be maximized.

The bug out placed the aircraft immediately in free fall with military thrust applied. Rolling inverted and applying positive G's is like being in a turn in the sense that the positive G bleeds energy.

The third situation was a defensive maneuver. At low airspeed and with someone directly on your 6 o'clock the pilot might try to "jink." Jinking was a last ditch maneuver where the pilot randomly pulled maximum G, and then went full negative G. I used this against an F-14 in a fight, and afterwards the pilot came and told me he couldn't get a firing solution.

As for uncontrolled flight there is the flat spin which can exert substantial negative G on the pilot. If I remember correctly a flat spin had never been positively observed in an A7-E. It was postulated, however, that given asymmetric wing loading it might be possible. On the other hand the F-14 could enter a flat spin. Talking with pilots who had knowledge about this sort of flight I was told that the negative G could be large enough where it would not be possible to get your hands on the ejection handle, either low or high. Not sure about the feet :)

An interesting side note. At times a pilot will find themselves in a high g turn, grunting against the inflated g-suit, and fighting the encroaching tunnel vision. When I found myself here I would pull on the stick a bit more and watch my peripheral vision go dark (tunnel vision). A bit more g and the tunnel got even narrower, until it was like I was looking through a hole. Then I would ease the stick and watch the hole get bigger. Pull back and smaller. Kind of interesting.