Stop particles from interesting?

You’ll see here,

there is quite a bit of intersection on these. i’ve tried turning on self effect but it doesn’t seem to do anything.

Particles may look like objects but they are really just points in space, they know nothing about object volumes. If you want to have non intersecting objects then you need to use rigid bodies

can they be used together so that I can generate my scene with the particle emitter?

I’m pretty sure there is a way to make the particles collide instead of go through each other. I would add a collision modifier under the physics panel for each object in the scene.

collision shape for particles is spherical… can make particles real meshes with Ctrl+Shift+A and convert to rigid bodies
or if you need animated objects can try this old script: