For the denoms $100/$500/$1000/$5000 do starting stacks of 10/6/6/2, that's 20k each, 400k in play. It will probably end no later than the 10k/20k level, at which point the $100, $500 and $1000 chips will have been colored off. The total value that's colored off is (10×$100+6×$500+6×$1000)×20=$200k, which is easily covered with the extra $5k and $10k chips.
If you want rebuys you'll have to reduce the stacksizes and therefore have shallower stacks. Just remember that you have to be able to cover the total chip count with the $5k and $10k chips (since all others will be colored off), i.e. you can't give out more than $500k total in startingstacks + rebuys. An example could be $10k stacks (10/6/6) with 1 rebuy OR add-on per player. That limits the total chip count to $400k, but you'll only start 100BB deep.
Levels:
100/100
100/200
100/300
200/400
(standard from here, but I'll give an example)
300/600
400/800
600/1200
800/1600
Color off $100
1000/2000
1500/3000
Color off $500
2k/4k
3k/6k
4k/8k
6k/12k
8k/16k
Color off $1000
10k/20k (should end before or during this level)
15k/30k
etc...
Now just calculated the level durations and breaks to fit your tournament length.