I work for a company very similar in size and seemingly in outlook to the person that asked the question. We were in the same situation a year or so back.
Our guidelines are:
* Don't charge for the quick 5 minute emails/phone calls. If I send multiple 5 minute emails in a day though to the same client I will bundle them into a single timesheet entry and bill it.
* Don't charge for the quick follow-up emails ("Did you get that done?", "I've had an urgent job come up. I'll be an hour later than I suggested" etc). These tend to (and should be) quick anyway
* Do charge for sending out answers. If I'm emailing instructions for doing something that the client doesn't know how to do then charge it. That's what the client pays you for - your expertise. It doesn't matter whether you are physically on-site, or whether you documented something for them in an email. The expertise is the same.
I found I cut my communication quality ever so slightly when we implemented this. I certainly still send the same number of communication updates and still take my time to thoroughly research and think about what I'm going to say. I no longer fret about exact wording as much as I used to though. My advise on those hard ones where you have to be careful about your wording - charge a reasonable amount of time, not neccessarily actual time spent. If you sent an email that should have taken 10 minutes to write, but it took 20 because you re-read it 5 times to make sure the tone was right - wear the other ten minutes. At least initially - you don't want to change overnight to charging for every minute spent. We wanted to remain reasonable. To me, this is just a cost of doing business.
Something else we formalised around the same time was documentation and planning. We generally weren't charging for time to document stuff. We now do charge a reasonable amount of time. Some of the documentation is for our own purposes so we don't charge that. We do charge for writing up environment configuration documentation though. We then provide a printed copy of it to the client each year when we re-sign the contract, so they can see where that time was spent.
Project management time is another area we weren't good at billing for. By this, I'm including things like calling a vendor to ask questions on the clients behalf, or calling their ISP etc. We now charge that, but are careful to let the client know in advance what the likely cost will be. We also try to be reasonable - if the vendor makes us wait on hold 30 minutes we would generally not charge all that time. Make sure you're doing something else while you're on hold though. And also make sure you mention the hold time in your timesheet entry, so the client can see that you spent that long but did not charge it.
That's my final suggestion - document your time better. I have a spreadsheet I have open all the time. It lists client, job details, start time, end time, auto-calculates total time and has a column for billable time (which defaults to total time, but can be overridden). Every time I start or end a job now I note it down in the spreadsheet. When you start seeing just how long you are spending on each task it will become clearer what you have to bill for and what you don't.
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