I have no personal experience with that incubator, but I see that someone else does have experience and gave a recommendation.
I hope it works well for you!
That sounds like it should work :)
(If it weren't for the two-incubator issue, I would not add any eggs over the next three days. As it is, yes that may be better than the alternative.)
One fairly simple way to manage staggered hatches: have two incubators. Incubate the eggs in one, then move...
Since you want the Silkies, I would definitely collect the first eggs, but once you get past about 2 weeks your chance of getting any pure Silkies will go way down.
If you don't think the Cochin is mating, you could just keep putting eggs in the incuator until you start getting ones that don't...
It's inconsistent.
Starting about the second day with the new rooster, you could get eggs fertilized by him. Or you could get eggs from the old rooster for a week or two (or in some cases even longer.) I think you could also get some of each, in mixed-up order, rather than just changing over at...