My daughter is getting married in Bali in May so we have already done our research. I would suggest you search in all the forums as there is a mountain of info available. For ease, she has decided they will actually do the legal bit at home, ie registry office and have a ceremony in Bali. The actual wedding is at a villa outside Ubud. No one else will know they are married except a couple of their friends who can't attend in Bali and will act as witnesses. The villa management will do all the arranging, ie minister, catering, flowers, arrange hair dressers etc. 10 family members will be staying there for a week with another 10 friends visiting for the actual wedding. The villa was decided upon basically so you don't have uninvited guests in their swim suits attending. This may not be an issue for you.

The Padma at Legian seems very popular if you want a hotel wedding.

Whatever you choose I'm sure it will be wonderful!