The silver and gold ones are gained from defeating villainous parties (those enemies with red auras around them) and are used to upgrade Mastery skills from completing Gravity Chamber missions, which become available during the 3 year training in the Cell Arc. You can also get them from using the Dragon Balls to wish for orbs, but I'd say that's ill advised compared to the other wishes.
50k is fine if you're still in the Saiyan Arc and not using up your healing item rations too much. You'll probably want to be around 100k or so by the time you get to the Cell Arc as upgrading the Gravity Chamber will be a highly expensive task (think it took 300k+ zeni to get it to Level 10 in the post-game). Clearing sub-stories and exploring the open world can help as both can offer selling items (the purple orbs that offer D Medals will sometimes be a rare item instead). Again, Dragon Balls can help, but the priority for wishes at first ought to be reviving dead villains. Later in the games, you'll be getting enough items from sub-stories that you can sometimes pawn off the sell-only ones for 50-100k if you've saved up a lot of them.
