What sets HBD apart from normal Sim Baseball games on WIS is the multiple-season nature of the game. Even if you're already out of the running for this year's division title, there's always next year.
That makes it important for you to keep an eye on your minors- making sure your top pitchers aren't running out there at 0(0) and your top position prospects are getting enough rest that they're not playing too far below 100% either.
It also makes it somewhat important to at least have some idea what you want to do with your team in the future.
I've found that it's helpful to put together a chart of who you have in your organization and when you're going to bring them up. I use Excel, but you can do it with anything that lets you put together a coherent list of positions and seasons.
The first thing to do is go through your organization and identify the guys at each level who have a reasonable shot to make it to the majors. Some of these guys will be stars, some might be good platoon players and some might be just a late-inning defensive replacement.
HINT: You can just write the word "prospect" in the "notes" section of their player card. If you don't use the notes for anything else, then you'll know that every guy who has the "note" icon next to his name is someone you consider a possible future MLer.
Next, figure out what positions they'll be able to play with some level of aptitude at the big league level based on their projected defensive ratings. You should probably set those positions now (even if their current ratings don't match up with the position) to make it easier to see on the depth chart where your organization might need some help down the line.
Then figure out when you think those players will first reach the major leagues. My rule of thumb is to give a guy roughly one season at each level, so the guys I picked in this year's amateur draft will on average reach the majors in Season 13, last year's draftees will play in Season 12, and so on. As I've said before, other people have different theories on player promotions and there is certainly no absolute answer, so you may have a very different timetable.
Once you've got a rough list of who'll be ready for the majors and when, you can fill your chart. I have it color-coded with guys who will be coming up for the first time mid-season in green, guys in their first three full ML seasons (when they're making the minimum) in white, guys who will be in their arbitration years in yellow, and guys who will be into their Free Agency years (5+ years of ML service) in blue.
HINT: Bringing players up for the first time in mid-season can give you an extra year with them at the league minimum. The number of games you need to wait after the start of the season is not very big (20) so if you can afford to wait a couple weeks, it may be worth it for your best prospects. For example, I brought Pedro Osuna up after my ML team played its 20th game this season. Now he won't be eligible for arbitration until the start of season 12. If I had promoted him immediately at the start of the season, he would have been up for arbitration at the start of season 11. If you're thinking about demoting a guy for 20 games mid-season to try to get back that service year, it may not be worth it-- many guys (especially those with lower makeup ratings) will see their ratings take a hit with a demotion.
Color-coding my chart helps me quickly see the places I may have holes in my organization and figure out when I might need to budget for more salary, trade an older guy for a younger one, etc. For example, if three or four of your starting pitchers all hit free agency during the same year, you may want to delay bringing one of them up by a year, trade one of them away for a younger player, budget a bunch of money for three big contracts, or make sure that you've got enough good prospects in your system to fill the holes if you let them leave.
It also my reveal that you don't have any legitimate major league-caliber shortstops or catchers in your system past next year, or that you have four ML-caliber third basemen who will be ready in the next two years, so you can trade a couple away to get more pitching.
Making charts seems like a very time-consuming process, but if you just update it once every off-season, it becomes very easy to manage and may prove to be a very valuable tool for your team in the long run.