I agree with Rob that it is not worth fussing over the areas that absorb more resin. However, if the unevenness bothers you, you can help even it out a bit by going over the whole boat with a roller several times while the resin is still wet. Don't add any resin, just roller everything. The roller will have a tendancy to pick up resin where there is a surplus and deposit it where there is a deficit.

This helps even out the coat a little and since you were probably standing around gawking at the beautiful color your wood just got, you aren't really wasting any time.

It is not generally a good idea to overwork the epoxy as it can introduce more air and humidity into it. But with a low-viscosity, blush-free type resin and a short mohair roller, the air is less of a problem and less air is introduced. If the resin starts getting tacky, quit messing with it.

I generally don't do a seal coat and I do all layers at once. This is not because it is neccessarily better to do it this way. It is more because I am lazy and anxious to get on to the next steps. Spreading out the process into more steps is probably "better". However, you don't want to let the epoxy set up too much before applying the next layer so timing can be tricky.

There are a wide variety of "good" ways of doing any task. The "best" ways all require that you be careful with every step.

: The advantage in using the sealer coat method is that it separates the
: struggle of the wood and cloth in their efforts to get all the resin they
: need and to expel and displace air. Sealing the wood in one step and then
: wetting-out the cloth in another separate step makes it easier to create a
: bubble free glass lay-up that is very transparent.

: I don’t bother trying to add more resin to the patches of wood that absorb
: resin faster because there is no way to keep from adding too much resin to
: the areas with a filled wet surface. If you try to add resin to the
: surface you will just create pools or sags of resin. The more you fuss and
: play with small areas of your boat the less uniform your coatings will be.
: And the less uniform your coatings then you must work more to sand uneven
: spots and the more you sand uneven spots the more irregular your surface
: will become.