thanks for your questions!
The arrow are overlapping due to the small column widths of the columns where it happens. You will need to insert longer contents into the cells of those columns (in at least one data row, not just the header row).
Or you could manually set a column width for each of those columns with the CSS example on Column Widths from the FAQ (http://tobias.baethge.com/wordpress-plugins/wp-table-reloaded-english/faq/).
Regarding your second question:
The table are stored as so-called options in the table "wp_options", with a name like "wp_table_reloaded_data_N".
They are serialized strings and under no circumstances should you edit the data in there directly, as you will corrupt the table (all its data and options)!
Resetting the ID counter is not easy at the moment, as there is no specific function for that in the plugin.
It is possible with PHP though, so if you are willing to do that, let me know and I can develop the necessary code.