Creating the seeds is the same, though like any seed-making, you do have to make sure you do your pollenization at least 4 weeks before harvest to ensure the seeds are mature.
But to be clear, there is a difference between "making seeds" (ie just putting pollen on a female plant) and "breeding" (combining plants genetics to isolate desired traits and stabilize them into offspring).
In terms of BREEDING with autos (vs regular plants), three differences come to mind:
-Since autoflowering plants cannot be maintained indefinitely in vegetative growth, you can't maintain mother plants or keep clones. This can make conventional backcrossing a little harder (you can do it with male pollen, if you keep some from desirable males), and in general, it makes mistakes more costly since you can't really "start over" with the same mother.
-If you're trying to cross autos with non-autos, realize that the most common (Lowryder-based) autoflowering trait is recessive. That means that you shouldn't expect to see any autoflowering plants in an F1 cross between an auto-and non-auto. Then, crossing those F1 plants to create an F2 generation, only 1/4 of the F2 plants would be expected to be autos. Of the 1/4 F2s that are autoflowering, roughly half will be male and half female. So on average you'd expect to have to grow EIGHT F2 offspring to expect to find ONE autoflower female, and in fact in the "real world" you may need more plants to pick from.
Now of course, in the real world, you're not likely to see *exactly* the ratios expected by pure Mendelian genetics, but the point is, you may have to run through quite a few F2s to find a few to carry on your breeding. If you want to actually do SELECTION from among a NUMBER of F2 females, you may have to grow out literally dozens of plants just to find a few to select from.
Not necessarily a big deal (you can grow them in large cups until sex shows, saving space, then preserve just the autoflowering females), but realize that large numbers may be at play here.
In general, smaller (ie ruderalis/dwarf) plants yield fewer seeds. On the other hand, they also take up less space, which makes breeding projects with autos more feasible for the average small grower.