I see two posible solutions.
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Use stretch and toss minimun 1 batter. When you choose to get that pitcher into the game, put him on warm up, without pitching to another batter. Then, get a mound visit and you could see your pitcher have a 3/4 of warm. Get that pitcher into the game and use the rest o warm up pitches to warm up him entirely.
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You could search on the options of the game that pitchers dont need to warm up. And when you get it into the game they are warm and without lose of stamina.
I use this strategy, but with the instructions of my first solution (stretching and tossing, then warm up with the mound visit)