Yes I understand your predicament. When I Interrailed for the first time I had little idea of planning travel and arranging accomodation. I made up my mind on my route from day-to-day and had a kind of meandering holiday without any unlucky no trains/accomodation situations but I recommend part-planning, with a broad overview and, if you will go to popular places during June/July/August, you should definitely book hostels or hotels.
There are internet hostel sites, on which you can arrange things really easily and cheaply. This takes a lot off your mind. In July I Interrailed for the third time and had all of my hostels booked in advance. This meant that I had little stress except for that of catching the trains.
Paris to Kortrijk gives you the opportunity to stop in Lille, which I understand is a nice place for a short visit.
I recommend that, unless a place is dull or dangerous, two nights/3 days everywhere gives you a chance to explore and recover from night train travel.
You could do some research on Lonely Planet's site to find interesting places that you might want to consider for your itinery. I'd recommend Grindelwald in the middle of the Swiss Alps, Central Berlin, Nice - Cote d'Azure, and Krakow and/or Prague.
I have a lot of pleasure from planning my trips and I'm sure you will.
Basically I have enough for about four months travelling (allowing for emergency money, etc) and I have a route idea which is fairly detailed in some places, but not in others. For example, I know exactly where I'm going in Greece and how I'm getting to Italy after that, but is it okay just to think, okay I want to get from Paris to Kortrijk, and not plan the exact trains, but just allow, say, two days for travelling there?
I haven't been travelling before and so I'm not sure on the estimates! Is there a guideline of how much time I should allow for travelling in relation to just seeing the sights? I don't particularly have to be anywhere at any time, but I'd like to stick vaguely to my route.