1) If you have an input file where other separators are used instead of -1 and -2 and you want to use SPMF, then you could just open the file in a text editor and replace the separators by -1 and -2 using the "find and replace" function.
Another way is to write a small program using any programming language to convert your file.
2) Now, if you want to see a different type of separator in the output file, then you could check the documentation of prefixspan: http://www.philippe-fournier-viger.com/spmf/PrefixSpan.php
apple | #SUP: 4 orange | #SUP: 4 tomato | #SUP: 4 apple | orange | #SUP: 4
As you can see in the above results, the -1 separator has been replace by | in the output file.
But this feature works in the GUI of SPMF.
3) If you want to modify the code of PrefixSpan andyou are a bit familiar with java, it is not very hard and you could find the -1 and -2 in the code of PrefixSpan and replace them by something else.
---- So that is the main idea. It could a good idea maybe to add a feature in SPMF to let the user choose a separator. This has not been implemented. But it could be a good idea for the future.