Usually, you can tell where the pause is without scanning the line, as it falls where there’s a clear break in the sense, such as at punctuation or before a conjunction. Where there’s no obvious break such as this, it is most logical to take your breath about halfway along the line, usually in the third foot.
sortibus Vergilianis, here are the first dozen lines of the third Aeneid:
Postquam res Asiae Priamique euertere gentem
immeritam uisum superis, ceciditque superbum
Ilium et omnis humo fumat Neptunia Troia,
diuersa exsilia et desertas quaerere terras
auguriis agimur diuum, classemque sub ipsa . . . . . 5
Antandro et Phrygiae molimur montibus Idae,
incerti quo fata ferant, ubi sistere detur,
contrahimusque uiros. uix prima inceperat aestas
et pater Anchises dare fatis uela iubebat,
litora cum patriae lacrimans portusque relinquo . . 10
et campos ubi Troia fuit. feror exsul in altum
cum sociis natoque penatibus et magnis dis.
Lines 2, 5, 7, 8, and 11 are easy: they have punctuation in them. Lines 1 and 10 similarly easy: the pauses fall before the conjunctions. Lines 3, 4, and 6 have misleading "et"s in them: we can hardly pause in the middle of elision, so for those, and for line 9, we’ll pause about halfway along. LIne 12 is an ugly one and rather tricky, as you are tempted to pause before “natoque” and “et”, but I think he’s really saying “with my allies and son, my icons and great gods”, and so I would rather put a single pause in the middle.
Postquam res Asiae ||| Priamique euertere gentem
immeritam uisum superis, ||| ceciditque superbum
Ilium et omnis humo ||| fumat Neptunia Troia,
diuersa exsilia et ||| desertas quaerere terras
auguriis agimur diuum, ||| classemque sub ipsa . . . . . 5
Antandro et Phrygiae ||| molimur montibus Idae,
incerti quo fata ferant, ||| ubi sistere detur,
contrahimusque uiros. ||| uix prima inceperat aestas
et pater Anchises ||| dare fatis uela iubebat,
litora cum patriae lacrimans ||| portusque relinquo . . 10
et campos ubi Troia fuit. ||| feror exsul in altum
cum sociis natoque ||| penatibus et magnis dis.
Note that only half of the lines here follow the usual rule of a third foot masculine caesura: in lines 2, 5, 7, 10, and 11 it falls in the fourth foot, while in line twelve we have a feminine caesura in the third. Note also how utterly unnatural it would be to put the pauses anywhere else in these lines.