if you cant use chipset lanes for, for example, your PCIe SSD, you'd have to put it in a slot that's wired into the cpu lanes, where the mobo & cpu combo will handle where the lanes go.
in an example:
forget that this is an asus maximus hero board for a brief moment, and imagine it's a super generic motherboard.
it's got a bunch of PCIe slots on it of vareous physical sizes, in order:
slot 1: 1x
slot 2: 16x
slot 3: not there because the GPU will cover it anyways, and it makes room for an M.2 slot.
slot 4: 1x
slot 5: 16x
slot 6: 1x
slot 7: 16x
now.. the 1x slots always get hooked into chipset lanes, because they're for stuff like wifi cards, etc. it's never anything high speed.
the first 16x slot is usually supplied with (all) 16 CPU PCIe lanes, and is destined to hold the GPU, if you plan to install one.
the second 16x slot (slot 5) is often 8 lanes electrically (meaning only the first 8 are hooked up), and will in cases where there's only 16 CPU lanes, share with the first slot, causing that one (slot 2) to run at 8x speeds when this slot (slot 5) is used as well. this is something that happens automagically these days.
as for the third 16x slot (slot 7).. thats where things get interesting. some board manufacturers make it a 4x slot that taps into (slot 5) in a similar fashion as it taps into (slot 2), meaning that if you use (slot 7), it'll cause (slot 5) to run at 4x, and (slot 2) to run at 8x.
some other board manufacturers tho.. take a different route, where that slot is hooked into 4 (or more if available) chipset lanes, and is destined to hold things like PCIe SSD's, dual- or quad NICs, or other medium-high speed perhiperal cards.
to know what goes where.. is usually a pretty deep dive into the motherboard manual, and sometimes other pools of information as well. if any mobo manufacturers are listening in, i'd be down for some printing on the board pointing out what goes where.