Your sentence was good, better than your second attempt. I would say "What is a reasonable percentage of design cost to total cost? " or "What is the reasonable percentage of design cost in the total cost?" But your sentence was fine.

Your first sentence is excellent, not only does it make sense, it is very well constructed. In the second sentence, you can't use "how many" with "design cost" because "design cost" is an uncountable noun. If you want to use 'how much', you could say, "How much of a percentage of design cost to total cost would be reasonable?" I replaced 'will' with 'would', because I assumed it was a hypothetical question. If it was a concrete question say, "How much of a percentage of design cost to total cost is reasonable?"\ However, your first sentence is so good, I wouldn't replace it.