I am typically on a Windows machine using multiple resources (and often still a phone call to 1-800-WX-BRIEF for CYA on TFRs, especially on the rare occasion I fly VFR) to plan an IFR flight, and I developed my planning/filing habits before iFly had the capability to file, so I do not use iFly for filing.
After doing my preflight planning using my variety of tools, I use FltPlan.com to file. I just flew a multi-leg trip this weekend, and filed the plans for all legs in advance. I have my (free) FltPlan.com account set up to send me texts and emails with alerts when plans are filed, and those alerts include an expected clearance, which in my experience matches the clearence I pick up about 80-90% of the time.
I also still like to print out the FltPlan.com nav log and put it on my kneeboard. Not really necessary with all the electronic redundancy and independence between devices in my cockpit, but it has useful info that's always available at a glance, and also some blank space to scribble in to capture clearances, ATIS reports, etc. I may one day use iFly's scratch pad feature for that instead, but my current tablet doesn't record my scribbles very well, so I'm still using old-timey paper today.
Congrats on your IFR ticket!