IIRC, the money for the 'public' residences of the monarch and the BRF [BP, Windsor, KP, SJP etc] comes directly from the taxpayer in the form of 'Grant-in-Aid' as it is known and not out of the Civil List payment made to the Queen. The problem though, as I understand it, that the sums paid have been cut back over the years in an attempt to save money, which means that routine and planned expenditure on maintenance has often been scaled back... After the fire at Windsor Castle in 2002, BP was opened to paying visitors [it had never been opened before] and parts of Windsor Castle previously free or off-limits were also opened. The originally intention was two-fold: one, to provide the necessary funds to restore the fire-damaged Windsor without calling on money directly from the taxpayer and secondly to allow people, albeit for a price, to see something more of the Palaces. Members here might well remember that at that time [the famous 'annus horribilis'], there was a general feeling that the RF was becoming remote and there were also complaints about the cost of the monarchy. IMVHO, I think that the period was unfortunate, because people were still getting over the death of Diana, which some people perceived as having been handled insensitively by the monarch, and also a general disenchantment with the activities of Sarah, Duchess of York, whose particular antics at the time were being used [fairly or unfairly] as a sort of 'stick with which to beat the monarch' After Windsor was repaired, the charges still remained in force and I understand the money is used to help maintain the Royal Palaces.
Balmoral and Sandringham are the Monarch's own properties and their care and repair is a matter for the Queen's own purse.
I am sure that more experienced members of TRF will be able to better supplement this information.
Alex