Looks like you didn't get the idea of timing.
First of all, it's tested and it works.
Second, AE set up to import depleted cells of both types and export fresh ones of both types.
Look:
:Advanced Machine: :Water Mill: :Wind Mill: - heat vents
:Uranium Cell: - double fuel rod, :Coal Cell: - empty double fuel rod
:Lava Cell: - quad, :Empty Cell: - empty quad
Initial load (simplified):
:Wind Mill: :Water Mill: :Wind Mill: :Water Mill:
:Water Mill: :Uranium Cell: :Lava Cell: :Wind Mill:
:Wind Mill: :Lava Cell: :Uranium Cell: :Water Mill:
:Water Mill: :Wind Mill: :Water Mill: :Wind Mill:
After 10-15 minutes replace slightly damaged dual cells :Uranium Cell: with fresh ones.
State after 2 hours 44 minutes (1 full cycle):
:Wind Mill: :Water Mill: :Wind Mill: :Water Mill:
:Water Mill: :Uranium Cell: :Empty Cell: :Wind Mill:
:Wind Mill: :Empty Cell: :Uranium Cell: :Water Mill:
:Water Mill: :Wind Mill: :Water Mill: :Wind Mill:
AE imports depleted quads (note the untouched doubles, because they're still have 15 minutes to burn):
:Wind Mill: :Water Mill: :Wind Mill: :Water Mill:
:Water Mill: :Uranium Cell:
:Wind Mill:
:Wind Mill:
:Uranium Cell: :Water Mill:
:Water Mill: :Wind Mill: :Water Mill: :Wind Mill:
AE exports new quads into two empty slots:
:Wind Mill: :Water Mill: :Wind Mill: :Water Mill:
:Water Mill: :Uranium Cell: :Lava Cell: :Wind Mill:
:Wind Mill: :Lava Cell: :Uranium Cell: :Water Mill:
:Water Mill: :Wind Mill: :Water Mill: :Wind Mill:
10-15 minutes later same repeats for doubles.
Again, it's tested and it works.
First of all, if your reactor has efficiency > 3.33 - then this is not a problem, as it produces more EU than it is required to generate uranium ore out of the matter.
Second, that's your job to automate production of fuel cells. To prevent filling reactor with 4 quads, use toggle bus and level emitters: If level of certain cells drops below limit, just turn off the cable that goes to reactor. And maybe light up a red lamp in control room.
For example, my closed/dedicated reactor supply line system consists of:
Mass fabcricator (constantly fed with scrap). 2 replicators - one for iron ore, one for uranium ore. 6 auto-workbench for crafting fuel, mox fuel, plutonium, dual uranium, quad uranium, dual mox. Macerator > Washer > Thermal Centrifuge. Metal former for iron plates > for cells crafting and fuel rods. Metal former for fuel rods. Canning machine. 2 uranium reactors, 4 mox reactors. Always keeps in stock 40 mox cells, 120 uranium cells of both types. Runs replicators when out of stock of anything.
Works like a swiss clock.