If your document contains indented text and you want to make sure that indent remains in the output, you need to take the following steps:
In PDF2XL Options > Conversion, place a checkmark in the box labled "Keep Text Attributes".
In PDF2XL Options > Format, place a checkmark in the box labled "Keep indentations".
On your source file in PDF2XL, select the column with indented text and right-click > Column Format in Output > Text. Note that the indentation will only work with a "Text" format.