The traditional way to go is using raw wheat in a cereal cooker, than adding it to the mash. Pierre Rajotte goes into great details about it in the book Belgian Ales (classic beer styles serie)
If you use flaked wheat, the wheat is pre-cooked for you and you do not need to cook it yourself and it can be added directly to the mash, but it will not produce the same exact flavor as the classic hoegarden for example.
Personally I always used the flaked wheat, I will try the raw stuff someday.. the problem is also that raw wheat is not that easy to find.
I use the flaked wheat too, wheat malt isn't the way to go in a wit, and raw wheat is hard to find and hard to use.
Here's one I made recently for a friends wedding that came out awesome...
Wit Wedding
Witbier
Type: All Grain
Batch Size: 6.00 gal
Boil Size: 7.58 gal
Boil Time: 60 min
Brewhouse Efficiency: 83.00%
Ingredients
Amount Item Type % or IBU
8.0 oz Rice Hulls (0.0 SRM) Adjunct 0.00 %
5 lbs 8.0 oz Pale Malt (2 Row) US (1.8 SRM) Grain 50.27 %
4 lbs 8.0 oz Wheat, Flaked (1.6 SRM) Grain 41.13 %
8.0 oz Oats, Flaked (1.0 SRM) Grain 4.57 %
7.0 oz Acid Malt (3.0 SRM) Grain 4.02 %
1.50 oz Crystal [3.50 %] (60 min) Hops 15.5 IBU
0.40 oz Coriander Seed (Boil 1.0 min) Misc
0.50 oz Orange Peel, Bitter (Boil 1.0 min) Misc
1.00 oz Citrus Zest (Boil 1.0 min) Misc
1 Pkgs Belgian Wit Ale (White Labs #WLP400) [Starter 0 L] Yeast-Wheat
Beer Profile
Measured Original Gravity: 1.055 SG
Measured Final Gravity: 1.008 SG
Actual Alcohol by Vol: 6.13 %
Bitterness: 15.5 IBU Calories: 242 cal/pint
Est Color: 3.3 SRM
Mash Profile
Single Infusion, Light Body
60 min Mash In Add 15.00 qt of water at 163.6 F 150.0 F
10 min Mash Out Add 9.00 qt of water at 203.8 F 168.0 F