Taken from the link below:
Seed Saving Instructions:
Morning glories will cross-pollinate. Gardeners should only grow one variety at a time to save pure seed, or isolate varieties by 1/4 mile. Seeds are ready to harvest when the seed capsules are completely dry and brown

Another option would be to plant some for early flowering, and then some for later and destroying any of the first ones that are still in bloom.

hth.

Sue...chemocurl

Here is a link that might be useful: Growing Morning Glory.

Sue,
You are partly correct. If the MGs are all regular MGs Ipomoea purpurea they will cross with each other. Like I. purpurea Milky Way and I. purpurea Grandpa Ott's will cross with each other.
The poster though has I. tricolor and I. nil. They will not cross.
I. tricolor Heavenly Blue and I. tricolor Blue Star cannot be grown together as they will cross.
I. nil is the Japanese type like Blue Silk or Hatsu Arashi so the Japanese types will cross with each other also.
It you want seed purity and not have to do any thing special in the garden, grow 1 I. purpurea, 1 I. tricolor, and 1 I. nil variety.
Sometimes though the species name on MGs is incorrect so it is always good to double check the species name.

Kim,
You are ok to grow them together : )
Remy

That's great! I really wanted to be able to plant both this season and be able to save pure seed. Thanks!
Kim