In most cases I assume that's correct - that is, weak acid gets quantitatively protonated. I know it may not work for strong acids (say pKa below 2, or 3) and in the case of diluted solutions (say below 10-4M) - in such cases to be sure (and if it matters) I check if the results are reasonable. In most cases I do it using ChemBuddy calculators (after all, I know how they work), but there are methods that don't require any software. Sorry, no time now to prepare an example - but in general you just have to check if the calculated values fit mass balances, charge balances and all equilibrium constants. If the assumption is wrong, results won't meet these criteria.