I do keep the seed from bee crosses, Jo Ann. I usually have multiple crossings on one stalk but never have all flowers hand pollinated. All my plants have numbers as my crossings do. Seeds from bee pollination are labelled with plant number and x (e.g. 64x) to clearly separate them from seeds originating from hand pollination. Any flower that is not labelled with a crossing number will automatically go into the plant number x bag after harvesting.
Both types of seed are sown out and cared for in the same way, but hand-pollinated seedlings are preferred if it comes to space limitations...