You can use the rrdgraph command line tool to generate graphs using the rrd files that MRTG generates. You can inspect he rrd file and see how soon it is consolidating the data, if it does this only after a day then you will loose the resolution that you are after. So basically I would for where MRTG stores the rra templates and the rrd graph templates.
It might take you a little time but since RRD is the backend graphing library/toolset for MRTG, Cacti, Munin, etc it is worth learning. I blogged about some things you might want to do when creating your own graphs on the Server Fault blog here.
Hopefully someone more familiar with MRTG can give you more details on your specific issue with MRTG.
Assuming you have no access to an upstream router or switch that provides the same view of this data that your ISP sees, you can use iptables accounting to on each host to count bytes/packets destined for anything other than your other IP address (or IP range), and then poke this into an RRD yourself.
EDIT
As an example, you could use some rules like these ones in iptables to create the accounting:
iptables -N ACCOUNT_IN
iptables -N ACCOUNT_OUT
iptables -I INPUT -j ACCOUNT_IN
iptables -I OUTPUT -j ACCOUNT_OUT
iptables -I ACCOUNT_IN -s ! 10.66.1.0/24
iptables -I ACCOUNT_OUT -d ! 10.66.1.0/24
This creates two new chains, ACCOUNT_IN and ACCOUNT_OUT. I then insert jumps to these at top of the INPUT and OUTPUT chains. Inside each chain, I add a rule with no jump target to match on remote addresses - for input, anything that doesn't have an address on my local /24 as source; for output, anything that doesn't have an address on my local /24 as destination. Packets then return from this chain back into your normal INPUT/OUTPUT chains, as there is no jump rule.
To check the accounting data:
# iptables -L ACCOUNT_IN -n -v
Chain ACCOUNT_IN (1 references)
pkts bytes target prot opt in out source destination
5 2138 all -- * * !10.66.1.0/24 0.0.0.0/0
# iptables -L ACCOUNT_OUT -n -v
Chain ACCOUNT_OUT (1 references)
pkts bytes target prot opt in out source destination
15 2846 all -- * * 0.0.0.0/0 !10.66.1.0/24
From there you can pull out those pkt/byte counts and pass to rrdupdate (I assume that you're OK with passing data into an rrd, as you've said you're ok with pulling data out of an rrd. If not, that question has probably already been asked here).
If you want to zero the counters each time you read them, pass the -Z command (zero counter) to zero the byte counters.
If any of your hosts are routers, you'll need to do accounting on the FORWARD chain as well - you can probably just insert a jump to both ACCOUNT_IN and ACCOUNT_OUT from the top of the FORWARD chain and it'll do the right thing, but I haven't thought about that enough to be 100% sure it'll work
Best Answer
RRDTool (as of version 1.4) does not allow you to have different scales on the Y-axis above and below.
What it does allow you to do is to create a secondary Y-axis with a scale shift argument. Items are still plotted according to the primary Y axis, though, so you need to perform any necessary calculations yourself. The necessary parameter is --right-axis.
http://oss.oetiker.ch/rrdtool/doc/rrdgraph.en.html