Good floorplan on the protoboard will also help you in debugging a design easily. Ten minutes of floorplanning will save an hour of debugging. Messy wires and components tend to hide fatal bugs. Try to test a chip before adding it to the circuit. If a chip is faulty, it should be thrown away after informing the TA or Steve.
Wires crossing over a chip only make it harder to remove if it is suspected of being faulty.
Double check the final design on the protoboard before applying power. Make sure all the chips have been wired up properly and all the right connections have been made. Learn to set up problems in logic analyzer before asking TA for help. TAs can only recognize signals rather than board design. Once problems are set up, bugs are easier to identify.