Thomas Freeman spent November and December, 1805, in Philadelphia, consulting with Robert Patterson about suitable scientific equipment for the expedition, and with Benjamin Smith Barton and Charles Peale about possible candidates for the role of naturalist. All three Philadelphians had helped train Meriwether Lewis in the winter of 1803.
While there, Freeman wrote a letter to his good friend and fellow surveyor, James McKee, who was then employed as an Indian agent among the Choctaws. In the first long paragraph, portions of which are now illegible, Freeman explains that he will set out up the Red River from Natchez, Mississippi, and that he expects to have with him a naturalist and an assistant astronomer, "if such persons properly qualified can be found here willing to hazard travel in the Neighborhood of St. Afee. [his italics]," indicating thereby that he and Jefferson had discussed that objective, though it was never publicly announced.
The next paragraph, above, conveys Freeman's enthusiasm and personal commitment regarding the expedition.
[A] Great many difficulties, and some personal danger will attend the exploration, but, I will--"Stick or go Through." The more danger the more honor. You see how I am kept afloat--an expensive turn when applied to me--Afloat!, and that's all--my savings do not more than float me through from job to job. But I hope ere long to flow into a permanency.
Evidently he had been led by Jefferson to expect the same sort of emoluments Lewis and Clark were to receive--some cash and some land. His base pay, possibly four dollars per day, was certainly generous in comparison with Lewis's captain's salary of forty dollars per month.
Based on Flores J&SE, 53-54 and note 76; 63-64