How do i transport items past a full chest

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Hey, it's you again ;D
First you "should" use punctuation marks for better understanding :p Second, not getting mad at me for teasing you ;)

You could use wooden transportations pipes to pump the chest empty, because i think, the quarry only uses one chest, not multiple ones. but i might be wrong here.
I suggest using diamon pipes to filter the valuables and barrels to store cobblestone, dirt and other junk.

EDIT: you can also put the output straight into pipes and then in a set of chests
 
I would have it... quarry > gregtech filter > trash > chests
...........................................\/
.............................diamonds/ores/valueable
|
For some reason the FTB forum does not like spaces..

But my quarries are rather small, and a diamond chest is sufficient.
If for some unknown crazy reason you're using oldschool chests, when using double chests I find it works better when connecting two pipes per chest. I've also found laying them flat out vs one above another to work better but YMMV.
 
Could we get a screen cap and which mod pack you're using? It's much easier for us to help with your problem if we can see your exact set-up and we know what you have to work with.

If I'm feeling lazy, I'll run a straight line of stone pipes out from the quarry, and then line each side with at least iron chests. What I have noticed with that is the first chests in the line always seem to end up with the most in them. If I'm doing a big enough dig and I'm still feeling lazy enough to do the bare minimum, I set up a pipe from the chests that are first on the line that feed into another group of chests. Honestly, if you're at that point it really is worth investing the 2 diamonds in 8 diamond pipes so you can control things without baby-sitting the quarry.