I have two T4A's, as I have different Direct sales businesses. When I try to edit the T2125, all are combined into one (in part 3A). How do I separate them.

TurboTax covers multiple businesses for one individual. Once you have completed the first business's income & expenses, choose the option to enter a new business. This should keep everything separated. 

Thank  you for choosing TurboTax.

The information from the 2nd T4A that is entered on the 2nd T2125 form does not show on that T2125, it is added to the first T2125 form.  How do I change this? Thanks

On both of your T4A's you have a box 20 or 48 with an amount?

Yes both T4A's have a Box 20 completed

Any amounts on your T2125 you should be able to edit. Where exactly are you seeing the amount on the T2125?

In Part 3A - Income reported on T4A slips
Should I remove from the T4A slip and put it somewhere else?

Unfortunately, when the income is coming from T-slips, the program will assign it to a particular T2125, and there no way to pick which one or move it to a separate one.