Multi city works well for what it is intended - trips consisting of visits to multiple cities

For trying to piece A-C via B via certain airports, it doesn't work so well

with multi city , it checks price and availbilty on a sector by sector basis(A-B and B-C , however this may not price up the correct fare for A-B and availability may also be different

Is the airport you want to connect at , valid for the journey which you are planning?