I've never actually manipulated any genes ever. I keep putting it off. I'm worried that it's going to add a wrong limb to one of my main allies and they will be screwed.
Just make sure to check the donor tables/donor limb counts. In most circumstances if the donor has the same number of a type of body part as the recipient, no new ones will be added-i.e. if you graft a normal human onto another one, no new limbs. Limb growth comes when the donor has more parts (i.e. putting an asura or horse into a human) or the recipient has fewer (i.e. putting almost anything into a bell).
The only penalties I'm aware of are for having >2 legs through gene engineering or for having >13 body parts in total. As long as you stay away from melding things with >2 legs into ones with 2 or fewer and don't go super crazy slapping things with lots of a single type of body part.
If you're playing on E+C and genuinely worried, there's a menu option to turn on savescum quickloading with F2, nothing wrong with having a safety net while you figure out how the system works. If all you're doing is buying slaves and melting them down to boost up your allies I can't think of anything bad apart from buying slaves that won't give anything because you don't know what they give yet... and they're 1-2k gold a pop, so that's hardly awful.