Currently you are confined to the container bound nature of using scripts within docs. If you create a new script inside outside of docs then you will be able to export information to a google spreadsheet and use it like a logging tool.
For example in your first code block
function setCheckboxes() {
// Add your spreadsheet data
var errorSheet = SpreadsheetApp.openById('EnterSpreadSheetIDHere').getSheetByName('EnterSheetNameHere');
var cell = errorSheet.getRange('A1').offset(errorSheet.getLastRow(),0);
// existing code
var checklist = SpreadsheetApp.getActiveSpreadsheet().getSheetByName("checklist");
var checklist_data_range = checklist.getDataRange();
var checklist_num_rows = checklist_data_range.getNumRows();
// existing logger
Logger.log("checklist num rows: " + checklist_num_rows);
//We can pass the information to the sheet using cell.setValue()
cell.setValue(new Date() + "Checklist num rows: " + checklist_num_rows);
When I'm working with GAS I have two monitors ( you can use two windows ) set up with one containing the GAS environment and the other containing the SS so I can write information to and log.