The way I usually deal with this scenario is to prefix the prompt name with a number, ie, 1) Enter Start Date; 2) Enter End Date. The prompts will now appear in the order you desire.
Just to clarify, if the prompts (filters) are created in the universe you can not control the order that they appear in a Webi v6 report. You can only sort if the prompts are created in the report. In Webi V6 the prompt order is random they are not alpha. This is a bug.