I use Family Tree Maker but I think the same conditions would apply to RootsMagic or any other program.
In FTM it is fairly easy to split of a part of your tree to share with others or for whatever reason you may have to split of a part of your tree. It can be very difficult to combine trees. The more individuals you have in the trees the harder it is. People duplicated in both trees do not always get merged. People with similar names and vital stats sometimes are merged even though they are two distinct individuals. It can become a major problem reviewing the combined tree to find these and other problems.
If you make paternal and maternal trees you may find individuals that belong in both trees. The brother of your paternal GG grandfather married the second cousin once removed of your maternal GGG grandmother. Now you have to start entering individuals in both trees. Every update you make to one tree you will have to check to see if it applies to the other tree.