The FamilySearch Blog recently posted an article by Lynne C. VanWagenen entitled, "Why Should I Put My Family Tree in More Than One Place?" Since I have always had more than one copy of my family tree in more than one program, this is not a problem or challenge for me. But I do frequently have to address the question of multiple family trees. The main issue, as mentioned by the article, is the concept of "keeping the information updated in all those places." Frankly, I do not find that issue a concern at all. I guess I should explain.
No matter how many family trees I have out there, and I have about a dozen or so I would guess, I only focus on and maintain one or at the most two programs as my "primary" database or databases. I do not try to keep the other family trees "up to date," I merely use them to gather sources and to attract contacts with distant relatives. I hesitate to mention any particular program or programs because my use of the program is not necessarily an endorsement. As I have written many times previously, I am always searching for the perfect program. Right now, there are a number of programs that I feel are perfectly adequate, but no one has yet developed the ultimately perfect genealogy program.
I would certainly advocate having your family tree on each of the FamilySearch.org Partner programs, i.e. Ancestry.com, MyHeritage.com, and Findmypast.com. The main reason I would take this position is the fact that each of these programs has well-developed record hint or record searching capabilities. Each of these programs provide a solid base of research that I would otherwise leave undone. It would be really nice, if these programs would synchronize their data with FamilySearch.org. But absent that feature, I find that the utility RecordSeek.com is an adequate substitute. If FamilySearch.org was finished with the process of transferring the data from new.FamilySearch.org, I would be persuaded to use the Family Tree program as my primary database. Absent the completion of the transfer process, I am compelled to use a standalone, desktop-based program as my primary database.
Bear in mind, that I am primarily Mac-based and so my choice of programs is somewhat dictated by that inclination. However, as with any of the online programs, I can use whatever program I choose.
I would strongly suggest reading the above referenced FamilySearch blog article. I agree with nearly everything in the article. I would point out that your ability to manage multiple programs with different commands in different file structures is probably the greatest challenge. Since I began recording my data in computers about 30 years ago, I have moved the data through a substantial number of programs. However, as time goes by and as the programs incorporate more media items, the process of transferring the data from one program to another becomes very complicated. Presently, there is simply no easy way to transfer all of the information in any one program to another program without some loss of data. The only time that there would be an exception to this rule would be if your data was very limited and you had no attached media, notes or other items that could be very program specific.
I do notice a couple of problems with the FamilySearch blog post. The MyHeritage.com program referred to is called quote Family Tree Builder. I think you should also know that these various programs have dramatically different user ratings. As I have in the past, I would recommend that you review the user comments in GenSoftReviews.com before buying a program.
To summarize, I essentially use one designated program as my primary database. Any information that I gather through the online programs or through my own research I add to my primary program. It is very useful if the program I decide to use also synchronizes with FamilySearch.org Family Tree. It is also helpful if the program is as full-featured as is presently possible. Not that I use all the features, but I do appreciate the ability to do so if I need to.