So I've got the hang of the Group races and breeding, but how would I go about prepping a horse to be well in the weights in a big handicap?

Ones on my list are

Melbourne Cup
Lincoln
All of the Royal Ascot Handicaps (the same year would be pretty impressive)
Northumberland Plate
Bunbury Cup
Stewards Cup
Ebor
Cambridgeshire
November Handicap
Cesarewitch
All three Ayr Cups

You need to race them lightly the more you race them the higher their rating gets
especially if you are targeting a handicap with a g1 quality horse. What I do when i target the
Melbourne Cup i run them in a maiden at 3YO usually at 1m5 or 6 with a small field I tell the jockey
not to go clear at the end and if they win they usually get a rating of 85 -90 i then target handicaps
0 - 90 0 - 95 0 - 100 I Try and keep their rating under 110 and run them in the ebor and then straight off to
Melbourne from there. Its about setting your target and tailoring the campaign to the target. Sometimes
once your horse hits the target handicap mark needed to get into big races you just have to stop racing them
and go straight to the target race hope it helps. Also using a claiming jockey helps if you horses gets rated too
High.

I can only comment on the Melbourne Cup as I only race on the Australian circuit (with the handful of international races)
For me I think 4yos have a good strike rate as you can get in under 59kg after your horse has had a good 3yo season.
After that you are relying on the horse's brilliance to win The Cup again.
I suspect I could get 3yo winners in The Cup but I usually concentrate my 3yos in their own age group/races.....Derby/Oaks etc

I find it easier to do when im properly up and running and have a solid string of horses coming out the breeding barn.

If for example I have 3 or 4 top stayers I like to aim a couple of them down the top handicap route instead of picking up group wins against each other. Maybe enter them in a couple of maidens over too short a trip at the start of their 3yo campaign and a low grade handicap. Then you can step them up in trip later in the year and target races at Royal Ascot like the King George handicap, then onto the Ebor and Melbourne cup if they remain well-in.

As Paul said above its key to set instructions in a horses maiden that they don't go clear, you can pretty much ruin a horses mark by them bolting up first time out.

If your horse is well in coming into Royal Ascot you should be able to win there and follow up again next time, like for a 7f horse the Buckingham Palace/ Bunbury Cup handicaps or 6f the Wokingham then Stewards cup.