The aim of installing a solar power system for most people is to make a profit and provide for your electricity energy needs over the next 25 years in a more cost effective manner than relying just on grid power. The falling cost of solar power and the availability of generous incentives such as the Federal Solar Tax Credit and the Net Metering law make this possible.
To do this you would ideally maximize the yield you would get from your solar panels. However, one thing you can't change is the direction and tilt of your roof and the overall size of your roof space.
What you need to do is work out which parts of your roof will produce the most amount of power. Here is a "discussion on the factors affecting how much power solar panels will produce".
To sum this up solar power production depends on the geographic location of your solar panels and also the direction and tilt of your roof. You can see how much solar energy you will produce given your location, specific roof direction and specific roof pitch by using this "solar power production calculator".
It is quite okay to use parts of your roof for solar panels that produce less power than the ideal south facing unshaded roof but the important thing is to know how much the power output will be reduced by and then to work out if these solar panels being installed on a sub-optimal roof will generate enough power to make the investment worthwhile.
kWh of extra production x Average rate paid for power / cost of additional kilowatt of solar panels
=% investment return on additional solar panels on non-optimal roof space.
Remember your average rate paid for power is likely to be much more than the base rate you pay for power. The other thing to remember is that utility power will increase over time so your investment return will also increase. You may want to use a higher average power price to reflect this when doing this calculation.
You simply need to decide if you are happy with this return for each part on non-optimal roof space.