Sounds like a viable plan. Do you have some generic, plain ammonia? If so, I would suggest the following;
Being a 5g tank with a built in filter it won't require much bio media. So, grab some from your FX6 and add it to the new filter.
Put the new substrate in first, then sprinkle some of your existing substrate on top.
Assuming you have access to ammonia and an API ammonia test kit (will have to get you the formula), bring the new tank up to 4ppm ammonia. Give it 1 or 2 days and then test for ammonia.
Add enough new ammonia to bring it back up to 4ppm (it likely will take very little in a 5g tank). Once enough bio builds up in the tank, it will typically remove the 4ppm ammonia within 24 hours.
This is step one. Once your tank is removing ammonia, now it's time to check for Nitrite. Kinda the same process - add 4ppm ammonia and let the bio media convert it to Nitrite. Once the Nitrite levels drop to 0ppm after 24 hours you are ready to add fish. How ling this process takes depends on many variables. If your bio media is pretty strong, it will take much less time. If you add some of your substrate on top it will take less time. If you add some of your plants it will take less time.
Entirely possible it could only take a few days to a week to get the tank ready for fish.
A lot of great reading in this thread. Near the bottom are some calculations if I remember right.
And just for the record, I really did add 80ppm ammonia to a bare 10g tank with just a sponge filter in it - and 24 hours later the ammonia was gone ;-)