Yes, you should plan for reentry if you'd like to land something big intact. Generally craft reenter like darts - heavy end forward (so center of lift will be behind center of mass).
If you have fins/winglets on the bottom of your lander, it will be almost impossible to reenter any other way than nose-first. So drop them with your boosters.
Other than that, if you'd like to reenter engines-first, then place all the heavy parts there (which will be mostly the engines, but crew compartments are also heavier than empty tanks or science labs). If you have parts which stick out (and produce drag), like the goo containers, try to put them closer to the nose.
Also, before reentry, if you have any fuel left over, transfer it to the tanks which are closest to the end you want to go first (so they are the heavier ones). To transfer fuel between tanks, right click on both of them while holding alt.
Trajectory is also very important for heating. Generally you'd want to spend quite a bit of time flying horizontally in the atmosphere to slow down. Altitudes below ~30km will very likely cook you at orbital speeds. Altitudes above ~40km might not slow you down enough for landing. So for reentry from the Mun or Duna you'd generally set your periapsis to about 35km, which should generally result in you slowing down to somewhere around 1km/s at those altitudes, and at that speed further descent will not heat you up significantly.
Note these numbers are for Kerbin, other planets have different atmospheres.
However, if you're coming back from, let's say, Jool, your speeds can be upwards of 4km/s, and you will cook even at 35km altitude. In those cases you would aim a bit higher, perhaps 45km, which wouldn't slow you down enough for a landing, but enough to not escape Kerbin again. And then slow down over multiple passes through the atmosphere.