this is why most people where i live never get any job like this done although their landscape could totally use it. they don't wanna spend $1000 or more on landscaping done correctly. they prefer just to spend like $100 and have you throw some mulch down even though the weeds will grow up through it since they have no paper down under it.
landscaping done correctly costs alot of money and takes alot of labor and man hrs to do. tell them your price upfront like you did. if they want more tell them the price will be alot more before you begin any extra work.
you don't have to always give an exact number. you can say it's gonna be in the $750-$1000 range. it's hard to pinpoint big jobs and it's hard to know how many hrs it's gonna take. you never know what you are gonna run into. explain that to them. just give them a range and don't go above the high point of that range on your bill. the range is to protect you. if you say $750 and then it takes you longer than you thought and costs more than you thought then you are out money. if you give a range you can charge $950 or whatever and everyone is happy in the end.