Here's a simple way to look at it....

Time base effects such as delays, chorus, flangers, etc...will sound better if ran through the effects loop...also eq's...

Other effects such as overdrives, distortions, and wahs will sound better in front between the guitar and amp.

This is how my effects sound the best to my ears.....

Try running your EQ-Flanger-Delay through the loop, in that order. Run the rest of your pedals in front of the amp. There is no golden rule, you'll just have to experiment to find what works best for your ears..