Grab yrself a short clean piece of tube or a blunt ended screwdriver. Put multiple zip ties on the lines. Put the tube or screwy against 1 of the ties farthest up from pump.  The idea is as you push the pump up into the tank, you push the lines in from a higher point to stop them crimping.

I regularly run my tank low and pull the filter to check/clean...this method is easy (just take yr time and be a little patient) and I have never crimped my lines.