It really depends on the property condition and how the price of the house compares to other sales. Honestly, if a house is priced reasonably, there is nothing wrong with paying full price. On the flip side, if it is worth$46,000 and it is priced at $90,000, an offer of $46,000 would not be too low.
The smart thing to do is to work with a Realtor. They can find out comperable sales in the area and let you know what it should be worth. They would also help you evaluate the condition of this property against the others sold.
Have you met with a lender yet? Right now, there is money to loan, but lenders are getting very "tight" with requirements, not just based on the buyers credit, but also based on the condition of the property and on how many houses you own.
The downpayment amount doesn't really effect the seller, but does make a difference on what types of loan you may be able to get.
If this is your fist house, or the first house you will have owned in the past two years, you may also qualify for the first time home buyers tax credit. If you buy the house for $46,000, you may be eligible for a check for $4,600 from the federal government (up to 10% of the sales price).
I hope that helps! Godd luck!