Hi Karen and welcome to the forum.
It is not unusual for PDF files to appear to be unformatted when converted to text. There are many PDF writers and different 'standards' over the years since PDFs were introduced. Remember that a pdf file is a formatting of a lot of not very formatted content!
Monarch offers various controls to assist people to create as neat an output as possible if the initial automatic assessment of the document is not quite able to interpret the contents as you need to see them. You could start be experimenting with them (actually start by reading the help sections related to them so you know what they are intended to do!) .
Sometimes you just can't get a consistent result, in which case there are techniques you can use with Monarch to overcome the anomalies.
Of course these are advanced techniques which are easier to understand when you have a little Monarch experience ...
... but as it the way of these things most newcomers seems to be pushed right in at the deep end and your case does not appear to break that tradition!
See what you can get from the format control. If you best result is not perfect let us know what sort of problems remain and we can guide you through the options for overcoming those problems.