breeding question with clydes

so I had a set of horses that not really knowing what I was doing I paired and bred them 2 times, well of course the 2nd foals all have better stats and from what I can tell better confirmation as well. so its getting close to time to pair the 2nd gens. so should I put the time in on breeding the first born foals or just the second born ones? I started with foundies and the goal is to keep the lines clean and breed down to 1 foal. 

Generally, if you do two sets of foals you'll do a "sell" foal and a "keep" foal, so you only have one set.  If you'd like to keep both horses, then keep the two foal sets separate and interbreed them however.  You'll end up with two foals from the same bloodline, just from different generations.  I generally breed twice each generation, and sell one foal each time. 

I will keep the ones that dont fit with the program just put  them with the general herd. and to make up the lost foals I have a set that I will wait till the last minute to breed them so I only have the one set of 2nd gen foals from them to match the ones I already have. jezz, that might be a bit confusing.