I don't follow. Is there an acrylic bond that's leaking (like a corner, the bottom, etc) or the bulkhead?
If it's an acrylic leak, yes you need to fix it with the correct material (16 dries up easy and is harder to patch with, 40 is better but more expensive). If it's the seal on the bulkhead itself, then it's a bad bulkhead/gasket or improperly installed/tightened. If it's a seal on the pipe going into the bulkhead, that's a plumbing issue with improper gluing or needs to be tightened and/or have some tape applied.
Never, never, never use silicone to "seal" a bulkhead. That's a rigged up solution that just masks the problem, and causes more harm than good.
Can you post a picture so we have a more accurate idea of what the issue is?