welcome. my advice is find a rehabber that has experience or you could partner with for a few deals until you gain more experience while keeping you out of major trouble.
here is an old post that may be of interest to you
http://www.biggerpockets.com/forums/48/topics/72801
Keep this in mind. you are rehabbing it to make money not for your taste or style which is probably why you and most people go over budget. No single item will ever push you over budget its just when you decide on a 100 different items and each time you go with the more expensive item you quicky can be a 20k over budget
Define, define define a scope of work . Be very detailed about what work needs to be completed. the more you can define what work needs to be done on paper the better off you will be. You can not just have ideas in your head and tell a contractor you want it to look like whatever. If you leave anything to interpetation then you will be disapointed 9 times out of ten. For example if you told me you wanted a pair of shoes and i the contractor came back with a pair of payless brown velcro shoes i suspect you may not be happy. You then would specifically tell me what kind of shoes you wanted. 1 pair of 4" high heel shoes that had to be black and size 7 maybe a certain designer name brand that you expect.
Go from room to room and write down everything that needs to be done. Then thing about the basics if you want a light here is there electrical there now or would electric need to be re routed to make your idea work. Make a running list for each room. then break down your list into categories such as electrical items, plumbing items, painting etc. Define what materials you need to complete your project. if its say drywall how many sq ft are needed? how many sqft of paint. quantites of material need to be defined. define if you will supply them or will the contractor.
ask questions when you dont understand. and even if you dont understand fully get a contractor to explain how many men and how many hours will it take to complete a specific job. if you have that basic info you can do some quick estimating. this simple estimating is great trick to feel if a labor only task is priced fairly.
example: it will take 3 of my guys 4 days to do what you are asking.
3menx8hoursx4daysx$50 per hour=$4800
So if you get an estimate of 12,000 you can quickly see your not in the same ball park and the estimate is high.
Spend time learning some of the basic trades such as plumbing electrical, carpentry. many things in residential construction are not hard to learn but spend some time learning those basics.
The more detailed you are, the better you define a scope of work, and the more organized you are the better your contractor will feel he can work with you and make money. if you are lazy and or dont want to deal with it because you dont know it, then your prices will be higher because they know there will be many changes that dont allow them to complete a task and move on. these kind of people waste a contractors time and it ends up costing them money on this job but costs them more money by preventing them from moving on to the next project where they can make money.
good luck