Commission is a share of what a rep sells, calculated as a rate applied to revenue, margin or units, so it moves with every deal. A bonus is a fixed amount paid for reaching a defined mark, so it pays in full or pays nothing. Most sales plans carry both, doing different jobs.
Both words get used for the extra money, which is how plan documents end up containing one and meaning the other. The mechanical difference is the shape of the payout curve. Commission is continuous: sell one more dollar and earn a fixed share of that dollar, at any point in the period. A bonus is a step: everything under the threshold pays zero and everything at or above it pays the same fixed sum. A rep sitting at 99% of a bonus target has earned nothing from it. A rep at 99% on commission has earned 99%.
Each shape is good at a job the other handles badly. Commission suits the case where more is simply better and every extra unit carries value, which describes most of a volume business. A bonus suits a specific outcome rather than a quantity: a certified installation, a product mix, a retention rate above a line, a project delivered by a date. Paying a rate on an outcome that either happened or failed to happen is awkward arithmetic. Paying a step function on continuous volume produces the cliff behaviour every compensation designer has watched at least once, where a rep at 96% in the final week spends credibility with a customer to drag one deal over a line.
In payroll the two usually land in the same bucket. US employers treat commission and most bonuses as supplemental wages, which is why withholding looks aggressive on a commission month whichever mechanism produced the money. The difference that matters is legal rather than fiscal: many US states protect commission once earned as wages, with rules about when it must be paid and what may be deducted, while a payment the plan describes as discretionary carries weaker protection. Which category applies is decided by the plan wording and the state, so a plan that calls something a bonus while calculating it as a rate per sale is worth rewriting before anyone tests it.
A rep with a $500,000 annual target. Under a commission plan they earn 5% of everything sold. Under a bonus plan they earn a flat $25,000 for reaching $500,000. The two designs pay identically at exactly target.
The 90% year is the one that decides the argument. A $50,000 miss costs $2,500 under commission and $25,000 under the bonus, and a rep who can do that arithmetic in November will behave accordingly, discounting included.
Plans often label a payment a bonus because the word sounds discretionary, then compute it as a percentage of each sale. The label does not change what the payment is. Where an amount is derived from one rep's own sales by a formula that rep can reproduce, most people and quite a few tribunals will read it as earned commission whatever the document calls it. Choose the mechanism on purpose, describe it in terms that match the arithmetic, and keep anything discretionary genuinely discretionary by tying it to judgement rather than to a rate.
The long form lives in the guides: Calculating commission.
Commish pays bonus vs commission the way your plan describes it, shows the arithmetic on every line, and traces each payment back to the deal that earned it.