I have only worked with relatively small orchestras, and in that time, one of the biggest problems is the combination of strings and woodwinds, especially in contrapuntal writing where the main voice is alternating between instruments. The woodwind section always seems to stand out, even if the strings are in a higher register, which can sometimes be a blessing, but is often a problem. In the exposition of the 1st mvt of my first symphony(pretty small orchestra, have written short orchestral pieces but this is the first that I intend to exceed 10 minutes) the first and 2nd themes are stated together in the mid string section, and those 2 themes are stated with different instrumentation 3 more times, and on the 2nd time the first theme is stated by the oboes and flutes, and the 2nd by the cellos and violas both in their high register. But this is the problem. These themes are supposed to collaborate, with the first theme being the more important theme at the beginning with the second as a supportive role, but the roles switch in the 2nd and 3rd phrase. But in this statement of the first 2 themes, the 1st theme, in all 3 phrases, dominates over the 2nd, with the 2nd playing as a supportive role. What should be done about this specifically, and overall, how do strings and winds interact in an orchestra?
Have you ever studied some orchestration manual? They may give you insights and tools to fix this. Korsakov, Casella, Blatter, Adler, Strauss & Berlioz, Thomas Goss... there's plenty of books on this topic. Orchestration can sometimes be seen as mix of problem-solving skills and colorize by numbers, but itself is an art form.
Said this, let's address your issue. As I can imagine due your given description, you're dealing with problems of balance and proper layering (front ground, middle ground and background). Although I cannot say much without seeing/listening to the score, maybe you can start to solve this thinking in your doublings and layers' textures. The front must have a feature to stand out in front of other layers (obviously), and this is usually a compositional problem, not an orchestration/arranging one.
Check doublings minding each sounding register of each individual instrument, chord voicings, counterpoint and general texture. If it's all ok in a non-orchestrated draft, expand this thinking in layers before everything else.
Each of these books have chapters on dealing with lack of balance and stability, and plenty exercises. Maybe you could profit practicing one or another.