The answer to this question is:
If the genetic engineering is performed as modifications in place to the existing genome, in such a way that genes are added and certain genes that all normal humans have must be modified or inactivated in both copies, then it is likely that a cross between an engineered and un-engineered human would be non-viable or in some way disadvantaged. This represents the simplest way of performing genetic modifications, basically by creating a new species.
However, there is another way...
An entire artificial chromosome may be added, with all the necessary genes to block expression of unneeded genes on the pre-existing chromosomes and to produce new proteins for the new functionality. This chromosome would need to exist in duplicate, the same as every other chromosome, so how could a cross between an engineered subject and an un-engineered subject be viable?
The answer to that is basically to engineer that in. There are several possible mechanisms, but they all amount to checking for the presence of two of the new chromosomes in a fertilised ovum, and either getting rid of any excess, or duplicating a single new chromosome.
Effectively, during meiosis, the new chromosome could be replicated twice by means of a new start-sequence and a modified initiator protein, and then if extra copies are present in the single-cell zygote, the extras could be destroyed by a targeted DNAse.
Alternatively, if the single-cell zygote had only one copy of the new chromosome, the new start sequence and modified initiator protein could start a round of DNA replication that would affect only the new chromosome.
Effectively, with this engineered new chromosome, even if only one parent possessed it, it would still be passed in duplicate to every child, with both copies coming from one parent. This would result in the new chromosome spreading rapidly through the population from generation to generation, as long as the modified and unmodified subjects are still willing and able to reproduce together.
Additionally, it could also be possible to engineer a mechanism by which engineered drugs could toggle the presence or absence of the new chromosome in gametes, so it could become a matter of choice - at least for males, since females produce all of their eggs prior to birth, at least in unmodified humans.