The key to managing a pitching staff is making certain you have enough pitchers with the right DUR/STA combos. My normal major league staff has 8 guys with starting pitcher stats and 5 guys with setup stats.
My top 5 starters go into the rotation while the other 3 get Long Relief roles. My top setup guy becomes the closer and the rest become setup or specialists.
Starters must have a minimum of 20 DUR and preferably closer to 30. They must have a minimum of 75 STA, the higher the better. I will occasionally use a starter with a high 60's stamina, but he better have DUR close to or above 30. And I will never use more than 1 on my staff. My 3 long relievers may have a couple guys with 60s STA, but again they better have high DUR and better have good stuff (splits., control, and pitches) to warrant my bending of the rules.
Setup/closer relievers need to have a DUR + STA combo of at least 90. This could be 70 DUR and 20 STA or could be 50 DUR and 40 STA. In addition, both the DUR and STA must be at least 20 each (no 95 DUR, 5 STA guys). Again, this 80 number is the bare minimum and I will try to get my ratings as high as possible.
When setting pitch counts, I start by setting each guy in his proper role and then using the Recommendeds. I normally leave the Recs alone for my starters. My long relievers I cut the Recs in half, usually going with somewhere between 30/35 and 40/45. My setup guys, I looks for a pitch count that roughly equals their STA (for example, a 25 STA guy may have a 20/20 or 20/25 count). This assumes the guy has a very high DUR (75+). if I am using a reliever with a lower DUR, I cut his pitch count down. Thus, a 55 DUR/40 STA guy will probably have a pitch count around 20/25 or at most 25/30.
I use the same formula for pitch counts in my minor leagues. Only difference is that at AA and AAA I increase to 4 long relievers and 4 setup, while at High A and Low A I use 5 long relievers and 3 setup. Rookie League I use 4 sets of tandem starters and a 9 man bullpen consisting of 4 long relief and 5 setup.
I rarely have to make Active/Inactive moves in the minors. I can probably count on one hand the number of times that i have ever had fatigue issues with my major league starting pitching staffs. It will still happen on occasion, normally associated with multiple extra inning games and a short starting stint or two, and in those cases I need to bounce my pitchers around a bit and maybe set a couple starter Call Bullpens down to 1 for a few games hoping to give my guys a rest. But with this system it ill eventually even itself out and I am fine. But for the most part, my pitching staffs run themselves with very little work ever needed.