http://www.guppiesonli.com/dfly/News/article/sid=15.html

Before we could more effectively answer your question we would need to know what each of your fish is carrying genetically. What kind of fry has the female dropped and what has the male sired? What characteristics are controlled by more than one gene?

Those are tough questions unless you are sure that each breeds to true to what the adult shows. You probably still would want to consult Guppy Designer and Guppywiki.

Some tips can be had here:
http://www.ifga.org/beginners/beginners_corner.htm
and in the IFGA library. I though that they had something more on line breeding.

As Scott L suggested Google line breeding and line breeding guppies. You will also find several hits and tips if you Google search Guppylog (upper right hand box) for line breading. In fact that calls up your comments. :)

It is not unusual to set up two lines. The guppies could have been from, let's say, the first batch that you saved from the female blue Japanese guppy and the male lyretail guppy, Breeders often save the second or maybe the third batch from a pair.)  You are going to need some tanks for this.

In the first crossings of brother to sister or maybe the male lyretail father to the most promising daughters, you would save a batch from each of the two matings. That means you have two tanks in addition to whatever is holding your original guppies.

You will split the males and females from each batch as soon as you can spot the female's gravid spot. That is another four tanks.

As those grow up you will select the best male or two males from line A and breed them to their most promising sister. You will do the same with the best one or two males and promising sister from line B. The males can then be returned to their brothers' tanks. The females could be left in their two tanks. When they drop you could return them to their female tanks or set them up with males again for a second batch.

You are now running somewhere between 8 and 12 aquariums for that one line of guppies. You will want to give away, sell or trade some of those older guppies. :)

One of the tricky things here is that I will bet that the females will not show lyretail. I think that female mollies will show that...

By the way, if you are Googling "breeding lyretails," make sure you are looking at something on guppies. In the case of lyretail swordtails, the fin rays of the male swordtails extend, like they do in the other unpaired fins (tail, dorsal...). They are unable to use their gonopodiums to fertilize females. Lyretail females must be crossed to regular male swordtails and their offspring mated in order to produce some swordtails (25%).

There are also long-finned strains of guppies. Some of those males are sterile too and the females must be back crossed with regular males of that color strain.

If you start out just line breeding one male guppy to one female each generation (rather than running two lines at first) please do start two lines at the third generation so as to avoid too much inbreeding.

One thing I saw suggested that you might get to your goal by the fifth generation - breeding all of them true. Or it could be the 25th generation. :0

That is why sometimes people are urged not to mix guppies of a specific strain with other guppies. (And as a batch of guppies in some shops are sold off, extras are often tossed into a tank with the extras from other orders in order to save space.) It is fun trying to guess what the crosses will produce.

But when a line, if it is "pure," is mixed with other guppies, the work of some breeder or breeders who worked several years to a couple of decades is down the drain.