Devices like the 3360 normally have 3 options for "PPP" settings:
1) PPP is on the modem
2) PPP is on the computer or router
3) Bridge Mode
The setting of "PPP is on the computer or router" works better for me than a setting of Bridge Mode.
If the 3360 has this option.......the Motorola 2210 does.....you might want to try that setting and keep the Time Capsule configured to provide the PPPoE credentials. Also check to make sure that the PPPoE settngs are adjusted for "Always On" on the TC.
It has been many months since I had a connection drop, and that was during a thunderstorm. But, I use a Motorola 2210 modem, so cannot say if the 3360 will behave the same.
We have found using a cheap as chips single port modem, like the TP-Link which cost about $25 makes bridge setup really easy.. it does depend on your distance to the exchange and what equipment the exchange uses which modem works best.. but for most people a cheap single port 2wire, speedstream, speedtouch/thomson/technicolor, tp-link which are easy to bridge and cheap to replace are often better than ISP modems, which for whatever reason, they don't want you to bridge.