Using multiple inputs is fine. As long as they are their own separate entities.
Example: I have 3 controllers. 1 USB throttle unit (CH), 1 analog gameport stick (MS), 1 analog gameport pedal set (CH).
The only problem is it takes more work to map which controls you want to which device, because in-game they are 3 different things. You have to switch back and forth to the different controllers to remap different switches. It's a minor price to pay.
You can take parts of some sticks and then re-build them so that your inputs go through the original boards, and it shows up as a "wingman" stick in windows, but really is your new custom rudder set. However, please note there are different voltages at work in analog and USB. Analog runs 5v through the inputs and the potentiometer varies that from 0% to 100%, and based on that voltage the system detects your input %. These are most often 100k (100,000) ohm resistance pots. USB systems use different (lower) voltages. They send a signal to the pots (usually 10k ohms if I recall) and it goes back to a circuit on a PCB that formats packets to be sent along a USB bus. You don't want to use the 100k analog pots with a USB board, so if you are building your own be sure to match the pots resistance to what you're doing (analog vs USB).
Also note that I have analog and cannot overclock my system at all. Not even slightly. If I do it screws up my gameport bus somehow. My stick totally spasses out, buttons don't work properly, etc. This isn't an issue for USB. One more reason to go that route.