beccad777,
The ladies are doing a terrific job of helping you talk through your options.

From what you've shared so far about your kiddos, I would be very hesistant to place your 3rd grade daughter in Preparing, as it requires strong reading skills since the child will be reading her own Independent History Study box readings and directions as well as her own science readings and all accompanying directions.

Even if she could somehow get through Preparing Hearts with much help, there would be little chance of her being able to read her own history and science in CTC the following year, as these are very challenging.
For that reason, I would definitely lean toward placing your two students in Bigger Hearts, if you desire to keep them together.

You would use the Extensions for your older son along with it. Bigger is targed for ages 7-9 with extensions for 4th and 5th graders. So, your son would technically fit in the Extension range of Bigger. I do think that there are quite a few skills in Bigger that would be good for your older child to have as well.
In looking ahead, It is not uncommon for students to use our guides for high school. So to use MTMM for grade 9 would actually work very well. We have families using our guides from CTC on up through MTMM for high school, with some adjustments and extensions. MTMM is targeted for ages 12-14 with extensions for 9th and 10th graders, so your son would be fine reaching MTMM in grade 9.

We also have 4 more guides to come after MTMM. Your son would just omit the final guide in the cycle for high school.
It will be important to add some things for your older son if you do desire to combine him in Bigger. He will need a higher level of grammar (probably Rod and Staff English 4), a higher level of spelling/dictation, a higher level of math, DITHR Level 4/5 with a book pack that matches him well, and possibly an additional writing program once weekly like Igniting Your Writing.
Your daughter should be able to do Bigger as written.

I'd advise English 2 for her as a good place to begin after FLL 1&2. We used FLL 1&2 with our own oldest son many, many moons ago.

Depending on her reading needs, she may need all or the last half or more of the Emerging Reader's Set. If you could share a few titles of some books she's currently reading that would help us advise you better in that area.
Feel free to share your thoughts!
Blessings,
Carrie