No you cannot mess a card up by enhancing with cards. However you can mess up an evolution by not enhancing the card to max before evolving. There are several methods of evolving to get more out of your card. Google Rage of Bahamut Evolving and you should see some pages that give examples of 4-2, 4-4, 6-2, 6-6, etc.
normal cards - one of the cheapest ways to enhance but yet it is slow and need many people to sell them to you.... which can get annoying if you have to trade them for it.
High Normal cards - these are a little better to use enhancing with, i recommend if your going to spend a lot on these, use it for a High Rare card(s).
High Normal with skills - these cards are very expensive in terms of rubies, becuase they can cost you around 3 hp ~300k each set, but with these you have a chance to raise up your High Rare's skill, which can go to lvl 10 skill.
Rares - these costs 2 hp-4 hp each, but if your looking to purely level up your cards skill, i recommend buying cheap rares to do that.
Angel Queens - these are most preferred if your only looking to enhance cards quick. these angel queens lvl up any card by 3 lvls a piece, so 1 = 3/2=6/3=9 etc.... these can cost 3-4 Hp each but you will waste no time at all max enhancing your most powerful cards.
Devil Queens - so far the best card to help raise a skill lvl up easy, although they can be quite pricey, there are very few out there..... prices can go from 5-15 HP depending on the seller.
-Hope this helps
Greatest Regards and continue to enjoy Rage of Bahamut.