In summary of what has more or less been conveyed here, the Juniata flows like this...
In general terms there are three branches of the Juniata. The Frankstown, the Little Juniata and the Raystown.
Frankstown comes down around Hollidaysburg and meets up with the Little J at Petersburg which is just west of Huntingdon. At this point it is the Juniata River.
The southern branch is the Raystown branch and it flows out of Bedford County and is the branch you can see when you drive the PA Turnpike. It flows NE to Saxton where it fills Raystown Dam. From the dam it flows another 5 mile or so where it meets up with Juniata just east of Huntingdon, just outside of Mill Creek.
The Little J is one of the best trout rivers in the state and has wild trout and fingerling stocking.
Frankstown Branch is pathway of the PA Canal (boats came up the Susquehanna the the Juniata at Clark’s Ferry). In the 1830’s before they figured out how to get a train over the Allegheny Plateau, Hundred ton canal boats were taken up the Juniata and then up the Frankstown Branch to Hollidaysburg. They were then loaded on a rail and winched over the mountains with huge ropes and 10 inclines - the Portage RR. An engineering marvel of the day and a National Historic site worth checking out if you ever head west on rt 22 past Altoona. The canal boats were then floated the remaining trip to the Ohio River watershed.