I don't think you need to worry about if you are using the latest version of LOOT with Fallout 3. The latest LOOT masterlist I'm looking at for Fallout 3 sets Merged Patch.esp and Bashed Patch, 0.esp at priority 80 so both will fall to the bottom of the load order. It also has a rule to load Bashed Patch, 0.esp after Merged Patch.esp.
Note that the LOOT's masterlist for Fallout New Vegas sets the priority of Bashed Patch, 0.esp to 80 but it does not have any rules for Merged Patch.esp. In this case, you'll want to add a rule to set the priority of Merged Patch.esp to 80. You'll also need to add another rule to load Bashed Patch, 0.esp after Merged Patch.esp once you create the bashed patch.