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Can't control the allies, unfortunately. What I do to make things go faster is use RegEdit to get all my characters to level 10, and that tends to take care of most monsters and some bosses in one hit before they even get a chance to attack.You could always get Elan up to Level 10 the natural way (takes 580 battles) but other characters only level up as part of the storyline and I don't think there's any natural way to get them over level 7, and Jota's permanently stuck at Level 2.
You CAN though it's not really necessary. losing is very difficult, though sometimes you have to do it to get some of the scenes. Viper's not really something you have to cheat at.