As a Resource Harvester, it is best hidden somewhere that it is easily defended, surrounded by other buildings. The Goo Factory should not be too high a priority beyond level 4 or 5 earlier on, since Goo isn't so important at an early stage and upgrading takes a long time. In fact, most people have 2x and sometimes even 3x more Goo then any other resource! If you have space, building multiple Goo Factories would be a quicker way to produce Goo faster. As your Goo Factory becomes a higher level, it will produce more Goo per hour, but its capacity will improve - allowing you to check back on it less and less. When you are Map Room 2 and level 38+, you have a constant need of Goo for making monsters, so investing is crucial.
If you reached or are reaching your maximum in Goo storage, you can "bank" your Goo in hatcheries. D.A.V.E.s and Zafreetis tend to be the most commonly used attack monsters, and also cost the most to produce, so fill up your Hatchery with as many of them so you don't max out your Goo storage. Note that if your Hatchery gets destroyed, the banked monsters will still be there after the Hatchery is repaired. But be careful: if someone happens to take over your outpost, THEY get all your monsters in your Hatchery. - Tparry