First of all, you should know this:
Low Search will always return channel entries.
If you're using a dedicated table to store your data, you might also be using your own set of template tags to display the output of that data, circumventing the
exp:channel:entries tag. If that is indeed the case, and there is no relation between your custom data and channel entries, then you can't use Low Search to search/display your data.
One way of creating such a relationship is to build a custom fieldtype that relates a channel entry with the data in your custom table. You can then use the search index API to generate custom data that is used in the Low Search index.
But the easiest route is probably changing your approach and do store the data in the exp_channel_data table. This makes things much easier to integrate. You can use the Channel Entries API to create/update/delete entries, extension hooks will be triggered when you do, so indexes are kept up to date automatically. Or you could use the same cron job to automatically re-index the Low Search collections.