Answer to your first question: it depends. If you enter the penalty at question level, in the Quiz Properties panel, it will be the total penalty whenever the user fails to enter the correct answer. There is another work flow, where you use the individual answer properties to define a negative score. Beware: you have to type in a negative number here, not a positive like for 'penalty'. That will allow you to give a different negative score for each wrong answer. The penalty will be dimmed in the Quiz Properties and calculated as the sum of the negative scores for the individual incorrect answers. That is perhaps a better work flow if you have multiple correct answers.
Sorry, forgot about the second question: not possible to transfer negative score. The end result for the quiz will be the sum of all scores, negative and positive. However a total that is negative cannot be transferred to all LMS's (depends on the SCORM version) and could be round to a zero score.