For starters, R&D agents have really lost their flair. IMO.
But let's cover your questions.
The authoritative answer:
To grind standings, you want to run normal missions (courier, indy, kill, command, security, whatever floats your boat) for the corp in which your target R&D agents are employed. For example, Lai Dai. I would recommend working your up way up to level 4 regular mission agents. As your standing with the corp improves, you are able to use more profitable R&D agents.
The single, silly, simple missions that the R&D agents hand out are mostly meant to double your research points for that one day. Again, a little personal injection here, those R&D missions are worthless. But hey, that should not stop you from trying a couple out, right? =)
I believe you can use a max of 6 mission agents - you have to train up Research Project Management to get that, though.
My experience with mission agents has shown me that they are simply more hassle then they are worth. First there is the time sink of raising your science skills up. If you have a science/invention/manufacturing alt, this may fit in nicely anyway - but this alt probably will not be running level 4 combat missions, right? Next, once you have 6 agents, not only do you have to consider what you want them to research, but chances are that they will be researching different things - I found it extremely difficult to find 6 high quality agents that research the same thing. In fact, I opted to go with a level 3 agent over a level 4 simply to grab a better datacore at the time. Which brings me to my final point.
Datacore prices have dropped drastically. At one point, you could pull in 300-400mil per month pretty easy on datacores with maxed out skills (or so I am lead to believe). I can only collect roughly 150mil every 3 or 4 months with my slightly-higher-than-average skills. On top of that, I have to travel about 40 jumps or so carrying somewhat bulky datacores around and trying to find a good place to sell them. If your main reason for doing datacores in the first place is isk, than datacores really suck. If you want them to make stuff, I personally believe it is far more satisfying and convenient just to buy them.
Just my two cents.