It depend to the structure of your compound. To me, the best method for the protection of the carbonyl groups is to convert them to acetal groups! but you have to know that this proticetion is done in acidic medium, so your compound must be stable in acidic medium!
In the end I recommend you to see the book entitled " green protective groups in organic synthesis". It can help you so much. you can download it from the following library site:
http://lib.free-college.org/
Yes, acetal is a best method for protection of carbonyl group. In a acidic media without any water by dialcohole, carbonyl compound convert to acetal.
If you are trying to avoid acidic medium, cyclic aminals may work for you. Aminals derived from many ethylenediamines form fast and without catalysis, even in water! Of course you will need some acid in order to perform the deprotection later, but it's also true for acetals.
Some literature:
Andrea Forster, Tanja Kovac, Hervé Mosimann, Philippe Renaud, and Pierre Vogel. Tetrahedron: Asymmetry 10 (1999) 567–571.
Alex Alexakis, Pierre Mangeney, Nathalie Lensen, Jean-Philippe Tranchier, Romain Gosmini and Sabine Raussou. Pure & Appl. Chem., Vol. 68, No. 3, pp. 531-534, 1996.
Good luck!
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