| Magus Black |
Yes both Skills gained from Versatile Training (and the one gained from the Advanced Armor Training's "Adaptable Training") use your Base Attack Bonus to determine Skill Ranks in those Skills.
Whether or not you had any Skill Ranks at all in the Chosen Skills is irrelevant. Any Skill Points you have already placed in those Skills are reimbursed to you so you can place them in other Skills.
IE: You are Level 10 and have 10 Ranks in both Intimidation and Bluff. You spend a Feat and gain a Advanced Weapon Training ability (via the "Advanced Weapon Training" Combat Feat), you select the default option of the Versatile Training option: Intimidation and Bluff.
These Skills now use your B.A.B. to determine the number of Skill Ranks they possess, as long as you stay using a Full-B.A.B. Class you can max out those skills without further investment. In addition to this the 20 Skill Points invested into those two Skills can now be shuffled into New Skills to expand your Characters options.
Also, justsoyouknow, any Skill chosen by above mentioned abilities become automatic Class Skills, therefore gaining the +3 Bonus that your other Class Skills offers (if they didn't already).