The rubber o-rings fell out of the fuel line, and I need to know what order they are supposed to be in so I can put them back correctly.

I assume you are asking what causes diesel drain-back? This is when a vehicle is not used for a while the fuel drains back towards the fuel tank leaving the fuel pipes empty and causes extended starting times or starting and then stopping or simply not starting.

It isn't unusual with some older vehicles. There are usually a number of nonreturn valves in the fuel system that are supposed to prevent it happening and in addition because it is supposedly an airtight system the fuel would usually be retained by outside air pressure.

A little wear here and there, a little erosion caused by microscopic particles in the fuel and a little corrosion from unavoidable nasty stuff in the fuel and after a while new things become old.
O rings stop being efficient and canister type fuel filters can be imperfect and allow air into the fuel lines.

Few diesel vehicles have a submerged tank mounted electric fuel pump but those that have are superior in these respects as they have a pressurised fuel line instead of a fuel line with negative pressure.

A common modification has long been to fit an additional inline nonreturn valve to prevent drain-back. These days it is more common to fit an inline hand-prime pump - a rubber bulb complete with nonreturn valves. preferably in the supply line from the tank to the filter.

if they are regular o-rings ( just plain rubber) then they can go back in place which ever way you want them to. If not, then you may want to look at your old filter and see how they went in

the same way you took it apart. put a little grease around the rubber seals so they will slide in easier. just tap on the fuel rail while lightly tapping it into place.

remove fuel from the tank
remove gas lines and tank straps

drop the gas tank and remove the pump from the top
reverse to reinstall

there are O ring seals, pull the injectors out and replace them all. the dealer can supply the parts, they are made from a special synthetic rubber so u MUST USE the correct parts from the dealer,.

the o ring is under neath the fuel pump in your tank. When you pull the fuel pump you will see a rubber ring come up with the pump. The ring stops moisture and dirt from getting in the tank. If your o ring is craked it could cause your jeep to run a little rough. I'm having the same problem in my jeep. I can not put the rubber ring on perfect. The rubber ring seems to be to big.

There is a rubber O-ring either on the end of the fuel line or inside the nipple.

The rubber ring goes between the tank and the pump/sending unit flange. There should be a nothc on the tank and a corresponding tab on the flange of the pump unit, to ensure correct orientation. Set the lock ring over the flange, and tap in clockwise with a NON_SPARKING drift. The ring will cam lock into place.

I did this job on my 3.1 about 2 months ago and i forgot to put the ("O") ring on back fuel rail. had a fuel mess!! had to tear down plenum to fix, in my case i lost the o ring on rail and forgot to put 1 on. I had to order 1 from chevy garage, and replaced it. cost 9.00 just for 1 little o ring. mine fit tight also!! see if o ring is ok, and check line. car runs fine!!

There are quite a few steps to this process and I would recommend you get the Haynes manual.