Yes. Ideally, your system should provide some safeguards. Just running a timer doesn't provide any.
1.
You want the power source to the acid pump to somehow be tied into the power source for the filter pump. This is so that even if the timer calls for acid, the acid pump can't run unless the filter pump is also running. This is to prevent a bunch of concentrated acid sitting in your pad plumbing and not going anywhere.
2.
A second safeguard has the same function, and this uses a flow switch. Power to the acid pump is not allowed unless the flow switch is closed. This is to prevent the same danger, but in case the power to the filter pump is available, but the filter pump is not actually running (like if it failed for some reason).
3.
A third safeguard is to ensure that the acid pump can't pump too much acid into the pool at once. Like if the timer fails to shut off the acid pump. This safeguard is more difficult to achieve. The IntellipH controller has this safeguard built in, as it only allows a few ounces of acid to be pumped at a time, but I suppose even it could fail. The ultimate way to achieve this safeguard is to minimize the available acid. The Pentair tank itself sort of has this built in, in that it only holds so much acid. About four gallons. If you follow the recommendation of cutting that to 1:1 dilution (half-strength acid), then the tank really only has about 2 gallons of acid at any given time. So even if you get a major malfunction, your pool will at worst get two gallons of acid in one shot, which will trash your pH for a time, but not cause any significant damage. Folks that hook up big Stenner tanks, or 50 gallon drums, are just asking for trouble.
Personally, I wouldn't trust any sort of digital timer alone for this task, and certainly not one of those manual timers. Either can get out of sync, or just fail, and without some or all of these safeguards, you're risking damage to your plumbing or your pool.
OK, that all said, it's possible one of your relays is actually coordinated to only close when the filter pump is running. That's how my Pentair automation works. So I just wired my acid pump power source to that. I actually use two relays: one for the power source, and one as the timer. So they both have to be closed for acid to flow. I also have a flow switch in the mix, for that added protection. So in your case, because you don't have an extra relay for the timing, you could do one or two safeguards: you could plumb in a flow switch, and wire that into your timer circuit. Or you could wire the acid pump power source up to the filter pump's relay, and then use a separate stand-alone timer for dosing, so that even if the timer called for acid, nothing would happen unless the filter pump was also powered on. Or you could do both (that's how mine is setup). You could use the pool circuit relay (that's what Pentair calls it), even if it's used for something else, even if it's not 24VDC, by using an additional stand-alone relay (I do something similar to that).
If you need a sketch of how to wire all that, I might be able to help, though I don't know anything about Jandy controllers. I expect they work similarly to Pentair controllers, but we'd have to verify that.
@santacruzpool could help, probably, if he'd check his TFP alerts once in a while, instead of binging YouTube videos all day long! (Oh, wait, I might be projecting!)
