Profit Factor is an abstraction of the group's mighty wealth. To a Rogue Trader, a bolt pistol is not something to be scrounged and saved for, like most of the Imperium's subjects - it's something to be bought in the numbers to outfit an army. Rogue Traders come from massive amounts of wealth, and regularly engage in acts of derring-do, piracy, and sublime contract-negotiation, all in the pursuit of greater material possession.
Profit Factor does not cover just money - it represents wealth tied up in land, trade deals, priceless heirlooms and artifacts, and so forth. It is these contracts and deals that make a Rogue Trader wealthy, not just coin. To save the massive amounts of bean-counting and Throne-pushing, Profit Factor is not counted by the coin - instead, it is given as dice.
1D - destitute (for a Rogue Trader)
2D - starting wealth for most Dynasties
3D - up and coming
4D - comfortably wealthy
5D - very well off
6D - rich by even the high standards of a Rogue Trader
7D - the most powerful Dynasties in the Expanse.
As a warning: operating on the "+1 pip per Endeavour" scale means that the players might only require 16 such Endeavours to get up to 7D. While this might be suitable for some of the larger-scale plots and plans, it leaves little room for the smaller deals.
To counter this, I suggest having Greater and Lesser Endeavours.
Greater Endeavours are grand, involved, difficult plots, which should be spread over multiple game sessions, with multiple objectives which contribute to the overall effectiveness of the plan. These should tax the Explorer's resources sufficiently, such as converting a whole system of planets to the Imperial Creed, or finding the final resting place of a legendary lost ship, or settling a long and arduous trade route through the Warp. These grant +1 pip (perhaps +2 for particularly nightmarish ordeals, or incredibly high-risk, high-reward deals, though these should be rare). A Greater Endeavour that grants a whole die to Profit Factor should be the basis of a campaign, more than a series of sessions - and is most likely easier to split into three 1-pip objectives.
Lesser Endeavours are somewhat more manageable - possibly even wrapped up within a session. Setting up a small trade route, setting up a Cold Trade business on a newly-founded space station, clearing a current trade route of a minor threat, or securing exclusive rights to the sale of a particular pattern of weapon to a Forge World would all fall under this banner.
Lesser Endeavours earn "points". Six points make up a "pip". GMs who wish a more light-hearted tone might even make each point a letter in the word "PROFIT" (this make for a great visual aid, writing up each letter as they approach the pip).
When a character wishes to acquire something, he rolls the group's Profit Factor dice against a Target Number - success means you can get your hands on it, failure could mean it is unavailable at that location, that it might take a few weeks to order in, or just that you can't find a merchant willing to sell it. Note that failure doesn't mean "you don't get it" - just that it's not instantly available. Each item will have an Availability in their stats, which will give you a TN for average purchase.
As a rough guide, common items and services don't need to be rolled for. Unless you're in the middle of bumfuck nowhere, you can walk into any Imperial city and buy a pack of lho-sticks, a laspistol and a cheap hooker. If you're looking to acquire, say, 100 laspistols, of a specific pattern and colour scheme, or hand-rolled cigars made from the dried remains of a particular type of Xeno plant, or perhaps a courtesan who looks like a specific Adeptus Sororitas Canoness (and is willing to act out your "Inquisitor and Heretic" fantasy), then you might need to roll. Bear in mind the respective tech-levels of the various Imperial worlds, however - on a Feral or Feudal world, a laspistol will be a one-of-a-kind treasure, whereas on a Forge World, they pump them out at a rate of tens of thousands a day.
Next: Gear and an Availabilty Chart!