Keep in mind that you have some flexibility, so what people offer as advise would be just that, their opinion. There isn't likely to be right answers out there, maybe just better and worse answers.
You want to start with the reason for implementing these systems, the function you want them to cover. That should provide some input as to what the scope should or shouldn't be.
With more details I could give a more complete answer, but it seems like overlap between the systems is a good thing, not a problem. You can use parts of 27001 that relate to 9001 as coverage for your 9001 system. With them serving different functions, quality versus information security, the overlap will be limited, but all the same I'd expect there to be some. Even if the same types of things are going on but the scope is different using standard procedures, standard document control, an internal audit process, etc. is going to make them work well together rather than to be a problem.
It would seem a shame to implement two different ISO systems covering overlapping scope and not integrate them to some extent, to not do the same things twice. All that aside, it may well make sense to limit scope to put that IT related services range out of scope of the system if it's not something you see as necessary to control in terms of quality.
It sounds like there could be a problem related to interpreting design and development, since you seem to be describing external design, but development would be a different thing. That's not what you asked about though, and again working from information fragments it's hard to extrapolate into details.
27001 isn't as complicated as it seems, although it makes sense to me to see the system in terms of levels, of doing different things at a higher organization level (more related to policy and general process) and then at lower level (more related to specific security controls), with a general process like risk assessment spanning the entire range. Here is a reference designed to work as a content starting point that might work to help explain it:
http://www.iso27001security.com/html/toolkit.html