Plan for a large base. At *least* 6x6 chunks. You will want 2x2 chunks for tree farm. Probably 2x2 chunks for food/biodiesel farms. I normally plan 1 chunk for an "automation room" with MV/LV autmation. This usually starts out as my steam tier room that I replace once I get mid-MV with LV/MV machines. Otherwise I plan ~ 1 chunk per tier. 2x2 chunks or more for large machines like EBF/pyros/etc. Don't forget about pollution, you might want to place really bad polluting machines on a far corner of your base. 6x6 is a nice size since it fits 4 3x3 chunk loaders.
You can also stack stuff inside of a single chunk if you want to conserve, but I like spreading my stuff apart and giving each area either piped power via liquid fuels or separate fuel sources in case of explosions.