How/What are you submitting that is it causing you problems? >>> I know that the search engines know what ip address the pages are submitted from
Yes, they do.
>>> and I think you can be penalized for it.
If you abuse it.
>>> The link exchanges between the sites will also be penalized because the engine now knows that they are from the same owner.
Yes and No. Excessive link exchanges Yes - and they can be on different servers/IP addresses and still receive the unwanted attention. It will be viewed as an attempt at false link popularity for rank manipulation.
Logical link exchanges, No. That is what the web is all about.
How can I submit to the engines with different IP (without using dialup)? Again - What and How often are you submitting?