Oh, I didn't realize what kind of save system you wanted. I didn't know you meant saving levels. The method I stated before is really easy for, say, saving the character's stats, which room he's in (like in Castlevania), and some other simple stuff which is stored in global variables and things. I see that you need something more than that, though and therefore, my response does not solve your problem.
BTW, I do believe there are some methods to encrypt files, though I have not yet looked into this very much myself. If you work on protection of save files (character stats and such, not levels), just keep in mind that everything can be hacked and therefore it is only worth adding so much protection and putting so much effort into it. If the person can't just open it with notepad and alter stats, that might be good enough. It's up to you.
Also, I agree with gammabeam that two people "coding" together in Construct does not work very well. You can get help from other people, but two people working on events for the same game at once is a bit...complex. You can't copy stuff between .caps.