One of the important things in fantasy football is to make sure that your defense isn't starting against your high-scoring offensive players, especially your quarterback. For example, if you had Tom Brady and the Houston Texans' defense on your team, you wouldn't want to start the Houston defense because if Tom Brady is doing well there's a good chance Houston isn't.
I'm wondering if a similar principle applies in fantasy baseball. In my head-to-head points league, I noticed that I have multiple instances where one of my starting pitchers is pitching against one or more of my batters. I'm I going to net less points? Will the points gained by batters significantly impact the points my pitchers get, and vice versa? Ultimately, Is it wise for me to play my starting pitchers against my batters?
Edit: Below I've added the scoring system for my league, per Jacob G's request. I'd be happy with a more general answer, since this becomes pretty localized. But this would be my specific case.
Note that lineups get set on Monday and cannot be changed until the following week.
**Scoring for Batting**
Categories Settings
Singles 1 point
Doubles 2 points
Triples 3 points
Walks (Batters) 1 point
Caught Stealing -1 point
Hit by Pitch 1 point
Home Runs 4 points
Strikeouts (Batter) -0.5 points
Runs 1 point
Runs Batted In 1 point
Stolen Bases 2 points
**Scoring for Pitching**
Categories Settings
Walks Issued (Pitchers) -0.75 points
Blown Saves -3 points
Complete Games 10 points
Earned Runs -1 point
Hits Allowed -0.5 points
Hit Batsmen -1 point
Innings 2 points
Strikeouts (Pitcher).5 points
Losses -5 points
Perfect Games 50 points
Quality Starts 3 points
Saves 7 points
Shutouts 15 points
Wins 10 points