how many varieties approximate are you talking about? is your problem the surface they would all take or something else?
consider a system like mine, also for germinating a decent number of varieties.
this is one of my boxes:
just nick one corner of the fabric or whatever is on the bottom, then map out the seeds on paper in relation to the cut corner. the biggest plus is being able to check for sprouting seed without unpacking and contaminating everything (just like you said), and that a lot can fit in one tupperware box.
and this is what not to do - forget to check on your seeds for a few days
luckily peppers are really hard to kill, they survived fine. coffee filters stop them from sticking, on cloth or paper they will hang on and then when you try to separate them you often break the root. which they can also survive, if it's not broken really high up, but better avoid.
notice the brown-purplish bit on the bottom of the pic that goes under the cloth and out of the box - this is a wick, which serves to protect the box from drying out on the heater. i pour some water into the bottom of the bag, the wick then draws a bit of that water and keeps the cloth moist. take something on experience, don't pour too much water, or the wick will draw too much and make a puddle in the box, in which all your seeds float and mix. duh.